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Form 10-Q uniQure N.V. For: Jun 30

July 29, 2026 7:17 AM EDT
0001590560--12-312026Q2false00-0000000(1) Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company's research and development in the Netherlands. (2) The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods presented.(1) Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company's research and development in the Netherlands. (2) The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods presented.(1) Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company's research and development in the Netherlands. (2) The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods presented.(1) Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company's research and development in the Netherlands. (2) The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods 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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington D.C. 20549

FORM 10-Q

(Mark One)

QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2026

OR

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from _______ to _______

Commission file number: 001-36294

uniQure N.V.

(Exact name of Registrant as specified in its charter)

The Netherlands

(State or other jurisdiction of incorporation or organization)

Not applicable

(I.R.S. Employer Identification No.)

Paasheuvelweg 25

1105 BP Amsterdam, The Netherlands

(Address of principal executive offices) (Zip Code)

+31-20-240-6000

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class:

Trading Symbol(s)

Name of each exchange on which registered

Ordinary Shares, par value €0.05

QURE

The Nasdaq Stock Market LLC (The Nasdaq Global Select Market)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes No .  

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).    Yes No .  

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company or an emerging growth company. See the definitions of “large accelerated filer” “accelerated filer” and “smaller reporting company” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer  

Accelerated filer  

Non-accelerated filer

Smaller reporting company 

Emerging growth company

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13 (a) of the Exchange Act  

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act.)    Yes No

As of July 24, 2026, the registrant had 69,366,412 ordinary shares, par value €0.05, outstanding.

TABLE OF CONTENTS

  ​ ​ ​

  ​ ​ ​

Page

PART I – FINANCIAL INFORMATION

Item 1

Financial Statements

2

Item 2

Management’s Discussion and Analysis of Financial Condition and Results of Operations

20

Item 3

Quantitative and Qualitative Disclosures About Market Risk

36

Item 4

Controls and Procedures

37

PART II – OTHER INFORMATION

Item 1

Legal Proceedings

37

Item 1A

Risk Factors

38

Item 2

Unregistered Sales of Equity Securities, Use of Proceeds, and Issuer Purchases of Equity Securities

40

Item 3

Defaults Upon Senior Securities

40

Item 4

Mine Safety Disclosures

40

Item 5

Other Information

40

Item 6

Exhibits

41

SPECIAL CAUTIONARY NOTICE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains “forward-looking statements” within the meaning of the federal securities laws. Forward-looking statements are based on our current expectations of future events and many of these statements can be identified using terminology such as “believes,” “expects,” “anticipates,” “plans,” “may,” “will,” “projects,” “continues,” “estimates,” “potential,” “opportunity” and similar expressions. These forward-looking statements involve known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity, performance or achievements to be materially different from the information expressed or implied by these forward-looking statements. These forward-looking statements include, without limitation, statements concerning: our financial position and performance, revenues, costs, expenses, liquidity, uses of cash and capital requirements; our need for additional financing or the time period for which our existing cash resources will be sufficient to meet our operating requirements; the success, progress, number, scope, cost, duration, timing or results of our research and development activities, preclinical and clinical trials, including the timing for initiation, completion or availability of results from any preclinical studies and clinical trials or for the submission, review or approval of any regulatory filing, including with respect to the Company’s Biologics License Application for AMT-130 to the United States Food and Drug Administration (the “FDA”) and Marketing Authorization Application for AMT-130 to the United Kingdom’s Medicines and Healthcare products Regulatory Agency (“MHRA”); the anticipated or ultimate outcome, and timing, of interactions with regulatory agencies, including the FDA and MHRA; our plans to conduct a confirmatory study for AMT-130; the timing of, and our ability to, obtain and maintain regulatory approvals for any of our product candidates; the potential benefits and clinical, therapeutic and commercial potential of our product candidates; our strategies, prospects, plans, goals, expectations, forecasts or objectives; the success of our collaborations with third parties; our ability to identify and develop new product candidates and technologies; our intellectual property position; our commercialization, marketing and manufacturing capabilities and strategy, including plans for potential commercialization of AMT-130; our ability to achieve long-term growth; and developments and projections relating to our competitors in the industry.

Forward-looking statements are only predictions based on management’s current views and assumptions and involve risks and uncertainties, and actual results could differ materially from those projected or implied. The most significant factors known to us that could materially adversely affect our business, operations, industry, financial position or future financial performance include those discussed in Part II, Item 1A “Risk Factors,” as well as those discussed in Part I, Item 2 “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and elsewhere in this Quarterly Report on Form 10-Q, as well as other factors which may be identified from time to time in our other filings with the Securities and Exchange Commission (the “SEC”), including our most recent Annual Report on Form 10-K filed with the SEC on March 2, 2026 (the “Annual Report”), our Quarterly Reports on Form 10-Q, Current Reports on Form 8-K, or in the documents where such forward-looking statements appear. You should carefully consider that information before you make an investment decision.

You should not place undue reliance on these forward-looking statements, which speak only as of the date that they were made. Our actual results or experience could differ significantly from those anticipated in the forward-looking statements and from historical results, due to the risks and uncertainties described in this Quarterly Report on Form 10-Q and in our Annual Report, including in “Part I, Item 1A. Risk Factors,” as well as others that we may consider immaterial or do not anticipate at this time. These cautionary statements should be considered in connection with any written or oral forward-looking statements that we may make in the future or may file or furnish with the SEC. We do not undertake any obligation to release publicly any revisions to these forward-looking statements after completion of the filing of this Quarterly Report on Form 10-Q to reflect later events or circumstances or to reflect the occurrence of unanticipated events. All forward-looking statements attributable to us are expressly qualified in their entirety by these cautionary statements.

In addition, with respect to all our forward-looking statements, we claim the protection of the safe harbor for forward-looking statements contained in the Private Securities Litigation Reform Act of 1995.

1

Part I – FINANCIAL INFORMATION

Item 1.Financial Statements

uniQure N.V.

UNAUDITED CONSOLIDATED BALANCE SHEETS

June 30, 

December 31, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands, except share and per share amounts)

Current assets

Cash and cash equivalents

$

413,027

$

80,240

Current investment securities

397,308

542,301

Accounts receivable

5,778

5,863

Prepaid expenses

10,245

20,506

Other current assets and receivables

7,911

7,076

Total current assets

834,269

655,986

Non-current assets

Property, plant and equipment, net

11,376

13,800

Other investments

30,267

30,237

Operating lease right-of-use assets

11,606

12,525

Intangible assets, net

62,101

72,790

Goodwill

24,587

25,355

Deferred tax assets, net

6,362

8,654

Other non-current assets

4,535

5,561

Total non-current assets

150,834

168,922

Total assets

$

985,103

$

824,908

Current liabilities

Accounts payable

$

4,979

$

5,170

Accrued expenses and other current liabilities

51,133

41,292

Liability related to pre-funded warrants

24,242

12,595

Current portion of operating lease liabilities

2,991

3,862

Total current liabilities

83,345

62,919

Non-current liabilities

Long-term debt

50,147

49,699

Liability from royalty financing agreement

489,333

473,199

Operating lease liabilities, net of current portion

9,696

9,832

Contingent consideration

18,113

18,736

Deferred tax liability, net

7,726

7,967

Other non-current liabilities, net of current portion

2,693

3,655

Total non-current liabilities

577,708

563,088

Total liabilities

661,053

626,007

Commitments and contingencies

Shareholders' equity

Ordinary shares, €0.05 par value: 100,000,000 shares authorized at June 30, 2026, and 80,000,000 at December 31, 2025, and 69,334,839 and 62,336,717 shares issued and outstanding at June 30, 2026, and December 31, 2025, respectively.

4,086

3,688

Additional paid-in capital

1,841,745

1,582,371

Accumulated other comprehensive loss

(58,251)

(58,222)

Accumulated deficit

(1,463,530)

(1,328,936)

Total shareholders' equity

324,050

198,901

Total liabilities and shareholders' equity

$

985,103

$

824,908

The accompanying notes are an integral part of these unaudited consolidated financial statements.

2

uniQure N.V.

UNAUDITED CONSOLIDATED STATEMENTS OF OPERATIONS AND
COMPREHENSIVE LOSS

Three months ended June 30, 

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands, except share and per share amounts)

(in thousands, except share and per share amounts)

License revenues

$

5,841

$

5,262

$

9,403

$

6,829

Total revenues

5,841

5,262

9,403

6,829

Operating expenses:

Cost of license revenues

(350)

(656)

(569)

(853)

Research and development expenses

(33,964)

(35,383)

(63,140)

(71,523)

Selling, general and administrative expenses

(17,367)

(13,500)

(37,435)

(24,408)

Total operating expenses

(51,681)

(49,539)

(101,144)

(96,784)

Other income

1,598

2,597

3,230

10,903

Other expense

(7,961)

(2,185)

(9,412)

(4,144)

Loss from operations

(52,203)

(43,865)

(97,923)

(83,196)

Interest income

5,051

3,524

10,280

7,651

Interest expense

(14,366)

(15,591)

(28,397)

(30,700)

Foreign currency (losses) / gains, net

(1,730)

18,638

(4,024)

25,810

Other non-operating (losses), net

(15,970)

(12,201)

Loss before income tax expense

$

(79,218)

$

(37,294)

$

(132,265)

$

(80,435)

Income tax expense

(1,841)

(425)

(2,329)

(921)

Net loss

$

(81,059)

$

(37,719)

$

(134,594)

$

(81,356)

Other comprehensive loss:

Foreign currency translation gains / (losses), net

1,634

(5,098)

(29)

(6,103)

Total comprehensive loss

$

(79,425)

$

(42,817)

$

(134,623)

$

(87,459)

Loss per ordinary share - basic and diluted

Basic and diluted net loss per ordinary share

$

(1.22)

$

(0.69)

$

(2.09)

$

(1.49)

Weighted average shares - basic and diluted

66,243,879

54,807,967

64,503,035

54,540,423

The accompanying notes are an integral part of these unaudited consolidated financial statements.

3

uniQure N.V.

UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT)
FOR THE THREE MONTHS ENDED JUNE 30, 2026 AND 2025

Accumulated

Additional

other

Total

Ordinary shares

paid-in

comprehensive

Accumulated

shareholders’

  ​ ​ ​

No. of shares

  ​ ​ ​

Amount

  ​ ​ ​

capital

  ​ ​ ​

gain / (loss)

  ​ ​ ​

deficit

  ​ ​ ​

equity / (deficit)

(in thousands, except share and per share amounts)

Balance at March 31, 2025

54,698,479

$

3,240

$

1,257,853

$

(53,805)

$

(1,173,602)

$

33,686

Loss for the period

(37,719)

(37,719)

Other comprehensive loss, net

(5,098)

(5,098)

Exercise of share options

5,312

44

44

Restricted share units distributed during the period

161,882

10

(10)

Share-based compensation expense

5,084

5,084

Balance at June 30, 2025

54,865,673

$

3,250

$

1,262,971

$

(58,903)

$

(1,211,321)

$

(4,003)

Balance at March 31, 2026

63,033,249

$

3,728

$

1,587,971

$

(59,885)

$

(1,382,471)

$

149,343

Loss for the period

(81,059)

(81,059)

Other comprehensive gain, net

1,634

1,634

Follow-on public offering

5,686,813

323

242,359

242,681

Exercises of share options

385,541

23

6,412

6,435

Restricted share units distributed during the period

229,236

13

(13)

Share-based compensation expense

5,016

5,016

Balance at June 30, 2026

69,334,839

$

4,086

$

1,841,745

$

(58,251)

$

(1,463,530)

$

324,050

4

uniQure N.V.

UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT)
FOR THE SIX MONTHS ENDED JUNE 30, 2026 AND 2025

Accumulated

Additional

other

Total

Ordinary shares

paid-in

comprehensive

Accumulated 

shareholders’

  ​ ​ ​

No. of shares

  ​ ​ ​

Amount

  ​ ​ ​

capital

  ​ ​ ​

(loss)

  ​ ​ ​

deficit

  ​ ​ ​

equity / (deficit)

(in thousands, except share and per share amounts)

Balance at December 31, 2024

48,988,087

$

2,945

$

1,173,068

$

(52,800)

$

(1,129,965)

$

(6,752)

Loss for the period

(81,356)

(81,356)

Other comprehensive loss, net

(6,103)

(6,103)

Follow-on public offering

5,073,529

261

80,250

80,511

Exercises of share options

21,240

1

202

203

Restricted and performance share units distributed during the period

782,817

43

(43)

Share-based compensation expense

9,494

9,494

Balance at June 30, 2025

54,865,673

$

3,250

$

1,262,971

$

(58,903)

$

(1,211,321)

$

(4,003)

Balance at December 31, 2025

62,336,717

$

3,688

$

1,582,371

$

(58,222)

$

(1,328,936)

$

198,901

Loss for the period

(134,594)

(134,594)

Other comprehensive loss, net

(29)

(29)

Follow-on public offering

5,686,813

323

242,359

242,681

Exercises of share options

410,849

24

6,796

6,820

Restricted share units distributed during the period

886,521

51

(51)

Issuance of ordinary shares relating to employee stock purchase plan

13,939

1

164

165

Share-based compensation expense

10,106

10,106

Balance at June 30, 2026

69,334,839

$

4,086

$

1,841,745

$

(58,251)

$

(1,463,530)

$

324,050

The accompanying notes are an integral part of these unaudited consolidated financial statements.

5

uniQure N.V.

UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Cash flows from operating activities

Net loss

$

(134,594)

$

(81,356)

Adjustments to reconcile net loss to net cash used in operating activities:

Depreciation and amortization

7,863

8,157

Amortization of discount on investment securities

(7,907)

(4,163)

Share-based compensation expense

10,106

9,494

Royalty financing agreement interest expense, net of interest paid

17,384

20,626

Deferred tax expense

2,329

921

Changes in fair value of contingent consideration

(82)

3,470

Changes in fair value of liability related to pre-funded warrants

12,201

Unrealized foreign exchange losses / (gains), net

8,329

(25,163)

Other items, net

(2,426)

(3,651)

Changes in operating assets and liabilities:

Accounts receivable, prepaid expenses, and other current assets and receivables

8,846

(6,761)

Accounts payable

68

(2,297)

Accrued expenses, other liabilities, and operating leases

11,064

(3,272)

Net cash used in operating activities

(66,819)

(83,995)

Cash flows from investing activities

Proceeds on maturity of debt securities

384,981

213,763

Investments in debt securities

(232,550)

(120,205)

Purchases of property, plant, and equipment

(612)

(386)

Net cash generated from investing activities

151,819

93,172

Cash flows from financing activities

Proceeds from follow-on public offering of ordinary shares, net of issuance costs

242,681

80,511

Proceeds from issuance of ordinary shares related to employee stock options and purchase plans

6,985

203

Net cash generated from financing activities

249,666

80,714

Currency effect on cash, cash equivalents and restricted cash

(1,906)

5,052

Net increase in cash, cash equivalents and restricted cash

332,760

94,943

Cash, cash equivalents and restricted cash at the beginning of period

81,801

160,329

Cash, cash equivalents and restricted cash at the end of period

$

414,561

$

255,272

Cash and cash equivalents

$

413,027

$

253,778

Restricted cash related to leasehold and other deposits

1,534

1,494

Total cash, cash equivalents and restricted cash

$

414,561

$

255,272

Supplemental cash flow disclosures:

Cash paid for interest

$

(11,494)

$

(9,652)

The accompanying notes are an integral part of these unaudited consolidated financial statements.

6

uniQure N.V.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1General business information

uniQure N.V. (the “Company”) was incorporated on January 9, 2012, as a private company with limited liability (besloten vennootschap met beperkte aansprakelijkheid) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics Holding N.V. (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability (naamloze vennootschap) and changed its legal name from uniQure B.V. to uniQure N.V.

The Company is registered in the trade register of the Dutch Chamber of Commerce (Kamer van Koophandel) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, its registered office is located at Paasheuvelweg 25, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000.

The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trade under the symbol “QURE”.

2Summary of significant accounting policies

2.1Basis of preparation

The Company prepared these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”) and applicable rules and regulations of the United States Securities and Exchange Commission (the “SEC”) regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates of the Financial Accounting Standards Board.

The unaudited consolidated financial statements are presented in United States (“U.S.”) dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parentheses, converted at the foreign exchange rate as of the transaction date.

2.2Unaudited interim financial information

The interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the period presented.

Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the three and six months ended June 30, 2026, are not necessarily indicative of the results to be expected for the full year ending December 31, 2026, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025 filed by the Company with the SEC on March 2, 2026 (the “Annual Report”).

7

2.3Use of estimates

The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities; the disclosure of contingent liabilities at the date of the financial statements; and the reported amounts of revenues, expenses, and tax-related items during the reporting period. Actual results could differ from those estimates.

2.4Accounting policies

The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2025, and the notes thereto, which are included in the Annual Report. There have been no material changes in the Company’s significant accounting policies during the six months ended June 30, 2026.

2.5Recent accounting pronouncements

There have been no new accounting pronouncements or changes to accounting pronouncements during the six months ended June 30, 2026, as compared to the recent accounting pronouncements described in Note 2.3.29 of the Annual Report, which could be expected to materially impact the Company’s unaudited consolidated financial statements.

3

Current investment securities

The following tables summarize the Company’s investments in government debt securities as of June 30, 2026 and December 31, 2025:

June 30, 2026

  ​ ​ ​

Amortized cost

  ​ ​ ​

Gross unrealized holding gains

  ​ ​ ​

Gross unrealized holding losses

  ​ ​ ​

Estimated fair value

(in thousands)

Current investments securities:

Government debt securities (held-to-maturity)

$

397,308

$

30

$

$

397,338

Total

$

397,308

$

30

$

$

397,338

December 31, 2025

  ​ ​ ​

Amortized cost

  ​ ​ ​

Gross unrealized holding gains

  ​ ​ ​

Gross unrealized holding losses

  ​ ​ ​

Estimated fair value

(in thousands)

Current investments securities:

Government debt securities (held-to-maturity)

$

542,301

$

308

$

$

542,609

Total

$

542,301

$

308

$

$

542,609

The Company invests in short-term U.S. and European government debt securities with high investment credit ratings. The U.S. and European government bonds are U.S. dollar and euro (€, or EUR) denominated, respectively. Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents and measured at amortized cost. Inputs to the fair value of the investments are considered Level 2 inputs.

As of June 30, 2026 and December 31, 2025, no expected credit loss was identified with respect to the investment securities.

8

4

Fair value measurement

The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820, Fair Value Measurement requires disclosure of the methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below:

Level 1 – Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date.

Level 2 – Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly.

Level 3 – Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable.

To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement.

The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Unaudited Consolidated Balance Sheets approximate their fair values due to their short-term maturities.

The Company’s material financial assets include cash and cash equivalents, restricted cash and investment securities. Cash and cash equivalents and restricted cash are measured at fair value using Level 1 inputs. Restricted cash is included in Other non-current assets within the Unaudited Consolidated Balance Sheets. Investment securities are measured at amortized cost.

9

The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of June 30, 2026 and December 31, 2025:

  ​ ​

Quoted prices
in active
markets
(Level 1)

  ​ ​

Significant
other
observable
inputs
(Level 2)

  ​ ​

Significant
unobservable
inputs
(Level 3)

  ​ ​

Total

  ​ ​

Classification in Unaudited Consolidated
Balance Sheets

(in thousands)

Balance at December 31, 2025

Assets:

Cash and cash equivalents

$

80,240

$

$

$

80,240

Cash and cash equivalents

Restricted cash

1,561

1,561

Other non-current assets

Total assets

$

81,801

$

$

$

81,801

Liabilities:

Liability related to pre-funded warrants

12,595

12,595

Liability related to pre-funded warrants

Contingent consideration

18,736

18,736

Contingent consideration

Consideration for post-acquisition services

638

638

Other non-current liabilities

Total liabilities

$

$

12,595

$

19,374

$

31,969

Balance at June 30, 2026

Assets:

Cash and cash equivalents

$

413,027

$

$

$

413,027

Cash and cash equivalents

Restricted cash

1,534

1,534

Other non-current assets

Total assets

$

414,561

$

$

$

414,561

Liabilities:

Liability related to pre-funded warrants

24,242

24,242

Liability related to pre-funded warrants

Contingent consideration

18,113

18,113

Contingent consideration

Consideration for post-acquisition services

617

617

Other non-current liabilities

Total liabilities

$

$

24,242

$

18,730

$

42,972

a)Contingent consideration

The Company is required to pay up to EUR 143.1 million (or $163.0 million based on the foreign exchange rate on June 30, 2026) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of the remaining contractually defined milestones related to the development of AMT-260 in connection with the Company’s acquisition of uniQure France SAS.

The fair value of the contingent consideration as of June 30, 2026 was EUR 15.9 million ($18.1 million) (December 31, 2025: EUR 15.9 million ($18.7 million)) using discount rates of approximately 10.1% to 11.8% (December 31, 2025: 11.8%).

If, as of June 30, 2026, the Company had assumed a 100% likelihood of AMT-260 advancing into a Phase III clinical study, then the fair value of the contingent consideration would have increased to EUR 51.3 million ($58.4 million). If, as of June 30, 2026, the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income.

10

The following table presents the changes in fair value of the contingent consideration (presented within non-current liabilities) between December 31, 2025 and June 30, 2026:

Amount of

contingent

consideration

(in thousands)

Balance at December 31, 2025

$

18,736

Unrealized change in fair value
(presented within Research and development expenses)

(82)

Currency translation effects

(541)

Balance at June 30, 2026

$

18,113

The Company classified the total contingent consideration liability as non-current as of June 30, 2026 and December 31, 2025. The classification of the contingent consideration within the Company’s Unaudited Consolidated Balance Sheets between current and non-current liabilities is based upon the Company’s best estimate of the timing of settlement of the remaining relevant milestones.

b)Liability related to pre-funded warrants

In September 2025, the Company completed a follow-on public offering which included the issuance of pre-funded warrants to purchase 526,316 of the Company’s ordinary shares at the public offering price of $47.50 per ordinary share, less a $0.0001 per ordinary share exercise price for each pre-funded warrant (“Pre-Funded Warrant(s)”). The obligation to issue ordinary shares upon the exercise of the Pre-Funded Warrants is classified as a liability related to pre-funded warrants.

The Pre-Funded Warrants are not exchange-quoted and are measured using a valuation technique whose significant inputs are observable; therefore, the fair value measurement is classified within Level 2 of the fair value hierarchy.

Liability related

to pre-funded

warrants

(in thousands)

Balance at December 31, 2025

$

12,595

Unrealized increase in fair value (presented within Other non-operating (losses), net)

12,201

Currency translation effects

(554)

Balance at June 30, 2026

$

24,242

5

Accrued expenses and other current liabilities

Accrued expenses and other current liabilities include the following items:

June 30, 

December 31, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Accruals for goods received from and services provided by vendors, not yet billed

$

24,684

$

20,490

Personnel-related accruals and liabilities (As of June 30, 2026, $7.2 million (December 31, 2025: $0.0 million) related to cash proceeds from employees' stock option exercises)

16,654

9,941

Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 7, "Royalty Financing Agreement")

5,778

5,523

Current portion of firm purchase commitment liability (including Genezen CSA termination payment)

3,808

5,102

Other current liabilities

209

236

Total

$

51,133

$

41,292

11

In April 2026, the Company entered into an agreement to terminate the commercial supply agreement (the “Genezen CSA”) with Genezen MA, Inc. (together with Genezen Holdings Inc., “Genezen”). Pursuant to the termination agreement, our obligation to supply HEMGENIX® and any minimum purchase commitments under the Genezen CSA terminate once contractually specified batches have been supplied. In connection with the termination, the Company wrote down the remaining carrying value of the intangible asset for the favorable supply terms under the Genezen CSA. The net effect of these items was recorded in Other expense, and did not have a material impact on the Company’s results of operations for the three and six months ended June 30, 2026.

6Long-term debt

The total principal outstanding as of June 30, 2026 under the Company's amended venture debt loan facility with Hercules Capital, Inc. (the “2025 Amended Facility”) was $50.0 million. The amortized cost, including interest due presented as part of Accrued expenses and other current liabilities, was $50.5 million as of June 30, 2026, compared to $50.1 million as of December 31, 2025, and is recorded net of discount and debt issuance costs.

The foreign currency loss on the loan facility in the three and six months ended June 30, 2026 was $0.5 million and $1.6 million, respectively, compared to a foreign currency gain of $4.3 million and $6.4 million, respectively, during the same periods in 2025. Interest expense during the three and six months ended June 30, 2026 was $1.4 million and $2.8 million, respectively, compared to $1.8 million and $3.6 million, respectively, during the same periods in 2025.

During the six months ended June 30, 2026, there were no material changes to the terms, available borrowing tranches, covenants, or collateral arrangements of the 2025 Amended Facility as described in Note 11, “Long-term debt” to the consolidated financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025. As of June 30, 2026, the Company was in compliance with all applicable covenants under the facility.

In July 2026, subsequent to the balance sheet date, the Company entered into an amendment to its loan facility with Hercules Capital, Inc. (as amended, the “2026 Amended Facility”). The amendment extended the period during which the Company may draw the $100.0 million term loan tranche from June 15, 2027 to September 30, 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility remained unchanged.

7Royalty Financing Agreement

During the six months ended June 30, 2026, there were no material changes to the terms of the royalty purchase agreement entered into in May 2023 (the “Royalty Financing Agreement”) with HemB SPV, L.P. (the “Purchaser”), as described in Note 12, “Royalty Financing Agreement” within the consolidated financial statements included in the Company’s Annual Report for the year ended December 31, 2025.

The following table presents the changes in the liability from the Royalty Financing Agreement for the period from December 31, 2025 to June 30, 2026:

  ​ ​ ​

Amount of liability

(in thousands)

Balance as of December 31, 2025 (includes $5.5 million presented as "Accrued expenses and other current liabilities")

$

478,722

Royalty payments to the Purchaser

(9,195)

Interest expense for the period

25,584

Balance as of June 30, 2026 (includes $5.8 million presented as "Accrued expenses and other current liabilities")

$

495,111

The Company records the debt at amortized cost using the effective interest method based on projected cash flows. As of June 30, 2026, the effective interest rate is expected to be within a range of 10.0% to 11.5% per annum (June 30, 2025: 12.0% to 13.5%). Interest expense recorded in connection with the Royalty Financing Agreement was $13.0 million and $13.8 million for the three months ended June 30, 2026 and 2025, respectively, and $25.6 million and $27.1 million for the six months ended June 30, 2026 and 2025, respectively.

12

8Shareholders’ equity

In June 2026, the Company received net proceeds of $242.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 5.7 million ordinary shares, at a public offering price of $45.50 per ordinary share.

In June 2026, the Company's shareholders approved an amendment to the Articles of Association increasing the Company's authorized share capital from 80.0 million ordinary shares to 100.0 million ordinary shares with a nominal value of €0.05 per share.

9Share-based compensation

The Company’s share-based compensation plans include the amended and restated 2014 Share Incentive Plan (as amended, the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of the Nasdaq Global Select Market with terms similar to the 2014 Plan (together the “2014 Plans”). At the annual general meeting of shareholders in June 2026, the Company’s shareholders authorized an additional 350,000 ordinary shares for issuance under the 2014 Plan. As of June 30, 2026, a total of 2,815,628 ordinary shares remain available for issuance under the 2014 Plan.

In June 2018, the Company’s shareholders adopted and approved the uniQure N.V. Employee Stock Purchase Plan (as amended, the “ESPP”) allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986, as amended. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the ordinary shares on each purchase date is equal to the lower of: (i) 85% of the closing market price on the offering date or (ii) 85% of the closing market price on the purchase date.

2014 Plans and ESPP

Share-based compensation expense recognized by classification included in the Unaudited Consolidated Statements of Operations and Comprehensive Loss in relation to the 2014 Plans and the ESPP for the periods indicated below was as follows:

  ​ ​ ​

Three months ended June 30, 

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

(in thousands)

Research and development expenses

1,888

2,758

3,865

5,221

Selling, general and administrative expenses

3,128

2,326

6,241

4,273

Total

$

5,016

$

5,084

$

10,106

$

9,494

Share-based compensation expense recognized by award type for the 2014 Plans as well as the ESPP was as follows:

Three months ended June 30, 

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

(in thousands)

Award type/ESPP

Share options

$

1,861

$

1,662

$

3,668

$

3,299

Restricted share units

3,255

2,547

6,461

4,760

Performance share units

(108)

875

(46)

1,435

ESPP

8

23

Total

$

5,016

$

5,084

$

10,106

$

9,494

13

As of June 30, 2026, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans was:

  ​ ​ ​

Unrecognized

  ​

Weighted average

  ​ ​ ​

share-based

  ​ ​ ​

remaining

compensation

period for

expense

recognition

(in thousands)

(in years)

Award type

Share options

$

14,464

2.57

Restricted share units

25,886

2.17

Performance share units

427

0.87

Total

$

40,776

2.30

The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares.

Share options

Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years. The first 25% of each grant vests one year after the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year. Any options that vest must be exercised by the tenth anniversary of the initial grant date.

The following table summarizes option activity under the 2014 Plans for the six months ended June 30, 2026:

Options

  ​ ​ ​

Number of ordinary shares

  ​ ​ ​

Weighted 
average exercise price

Outstanding at December 31, 2025

4,531,991

17.04

Granted

869,760

$

11.48

Forfeited

(12,451)

$

9.58

Expired

(16,186)

$

37.84

Exercised

(410,849)

$

16.60

Outstanding at June 30, 2026

4,962,265

$

16.05

Thereof, fully vested, and exercisable on June 30, 2026

2,769,675

$

19.77

Thereof, outstanding and expected to vest after June 30, 2026

2,192,590

$

11.35

Outstanding and expected to vest after December 31, 2025

1,999,315

$

11.81

Total weighted average grant date fair value of options issued during the period (in $ millions)

  ​ ​ ​

  ​ ​ ​

$

6.4

The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions:

Three months ended June 30, 

  ​ ​ ​

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

Assumptions

Expected volatility

95%

80%

95%

70% - 80%

Expected terms

10 years

10 years

10 years

10 years

Risk-free interest rate

4.68%

4.64%

4.21% - 4.68%

4.36% - 4.64%

Expected dividend yield

0.0%

0.0%

0.0%

0.0%

14

RSUs

The following table summarizes the RSU activity for the six months ended June 30, 2026:

RSUs

  ​ ​ ​

  ​ ​ ​

Weighted average

Number of

grant-date fair

ordinary shares

value

Non-vested at December 31, 2025

2,395,420

$

12.15

Granted

1,112,250

$

12.36

Vested

(886,521)

$

12.29

Forfeited

(113,350)

$

16.22

Non-vested at June 30, 2026

2,507,799

$

12.01

Total weighted average grant date fair value of RSUs granted during the period (in $ millions)

$

13.8

RSUs are measured at grant date based on the market price of the Company’s ordinary shares and, except for certain grants made to non-executive directors, vest over a three-year period. RSUs granted to non-executive directors vest one year after the date of grant.

PSUs

The Company granted PSUs to certain employees in 2024 and 2026, that, with respect to the 2024 PSUs, would have been earned upon the Board of Directors’ assessment of the level of achievement of an agreed upon performance target, and, with respect to the 2026 PSUs, will be earned upon Company management’s assessment of the level of achievement of agreed upon performance targets, subject, in each case, to the grantee’s continued employment. The fair value of PSUs granted in 2024 and 2026 was determined on the grant date by reference to the market price of the Company’s ordinary shares.

The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. As of June 30, 2026, certain 2026 PSUs were assessed as probable of achieving the requisite performance condition.

As of June 30, 2026, the Company determined that the performance target for the outstanding 2024 PSUs were not met within the contractually defined performance period and were consequently forfeited.

The following table summarizes the PSU activity for the six months ended June 30, 2026:

PSUs

  ​ ​ ​

  ​ ​ ​

Weighted average

Number of

grant-date fair

ordinary shares

value

Non-vested at December 31, 2025

22,500

$

15.40

Granted

28,750

$

22.40

Vested

$

Forfeited

(22,500)

$

15.40

Non-vested at June 30, 2026

28,750

$

22.40

ESPP

During the six months ended June 30, 2026, 13,939 ordinary shares were issued under the ESPP compared to nil ordinary shares issued during the same period in 2025. As of June 30, 2026, 72,773 ordinary shares remain available for issuance under the ESPP compared to a total of 86,712 ordinary shares as of June 30, 2025.

15

10

Segment reporting

The Company is advancing a pipeline of innovative gene therapies seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company manages the operations related to these research and development activities within one operating segment because they rely on a common set of infrastructure, resources and technology of the products and production processes, types of customers, distribution methods and regulatory environment.

The leadership team is identified as the Chief Operating Decision Maker (“CODM”).

The CODM allocates resources to research projects and clinical candidates based on scientific data as well as quantitative and qualitative expected risk-adjusted returns on investment. The CODM uses segment operating loss to monitor that cash operating losses remain within the approved budget.

The accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. 

Three months ended June 30, 

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

2026

  ​ ​ ​

2025

(in thousands)

(in thousands)

Revenue

$

5,841

$

5,262

$

9,403

$

6,829

Less:

 

 

Employee related expenses

 

(16,960)

 

(14,525)

 

(33,746)

 

(28,741)

Laboratory and development expenses

(17,387)

(15,593)

(32,148)

(31,560)

Professional fees

(1,756)

(3,124)

(6,263)

(5,181)

Information technology system costs(2)

(1,427)

(838)

(3,086)

(1,839)

Facility expenses

(1,437)

(1,704)

(2,984)

(3,371)

Other segment items(1) (2)

(2,511)

(1,804)

(6,024)

(2,773)

Segment operating loss

(35,637)

(32,326)

(74,848)

(66,636)

Reconciliation

Depreciation and amortization expense

(4,907)

(3,630)

(7,863)

(8,157)

Share-based compensation expense

(5,016)

(5,084)

(10,106)

(9,494)

Fair value (loss) / gain - contingent consideration

(1,256)

(2,254)

82

(3,470)

Fair value loss - Liability related to pre-funded warrants

(15,970)

(12,201)

Foreign currency (losses) / gains, net

(1,730)

18,638

(4,024)

25,810

Interest income

5,051

3,524

10,280

7,651

Interest expense - Royalty Financing Agreement

(12,963)

 

(13,770)

(25,584)

 

(27,079)

Interest expense - Hercules loan facility

(1,403)

(1,821)

(2,813)

(3,621)

Other reconciling items

(5,387)

(571)

(5,188)

4,561

Consolidated loss before income tax expense

$

(79,218)

$

(37,294)

$

(132,265)

$

(80,435)

(1)Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands.
(2)The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods presented.

16

11

Other investments and concentration of credit risk

The following table summarizes the Company’s other investments as of June 30, 2026 and December 31, 2025:

June 30, 

December 31, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Carrying amount of equity investments

$

15,143

$

15,615

Convertible note receivable

15,124

14,622

Total

$

30,267

$

30,237

The Company holds investments in non-publicly traded equity securities without readily determinable fair values. These investments are accounted for at cost, less impairment and adjusted to fair value if there are observable price changes in orderly transactions for identical or similar investments using the measurement alternative in accordance with ASC 321, Investments – Equity Securities. The carrying value of these investments as of June 30, 2026 and December 31, 2025 was $15.1 million and $15.6 million, respectively, and are presented within Other Investments in the Company’s Consolidated Balance Sheets.

The Company did not recognize any upward adjustments, downward adjustments, or impairments relating to investments carried under the measurement alternative during the three and six months ended June 30, 2026, and 2025.

Genezen

In 2024, as part of the Company’s divestment of its commercial manufacturing operations to Genezen, the Company entered into various service agreements including the Genezen CSA.  In April 2026, the Company entered into an agreement to terminate the Genezen CSA. Pursuant to the termination agreement, the Company’s obligation to supply HEMGENIX® and any minimum purchase commitments under the Genezen CSA terminate once contractually specified batches have been supplied.

The Company’s prepayments for services to be received amounted to $5.7 million as of June 30, 2026, compared to $13.9 million as of December 31, 2025. In addition, as of June 30, 2026, the Company holds a convertible note receivable of  $15.1 million which is due in September 2029 and for which Genezen is the counterparty (December 31, 2025: $14.6 million).

These balances represent a concentration of credit risk, and the Company’s maximum exposure to loss is the carrying value of these assets. No expected credit losses were recognized during the three and six months ended June 30, 2026 or 2025.

CSL Behring

As of June 30, 2026 and December 31, 2025, accounts receivable from CSL Behring LLC (“CSL Behring”) totaled $5.8 million and $5.9 million, respectively, in each case related to royalty revenue which is included in License Revenue in the accompanying statements of operations and comprehensive loss.

12

Income taxes

The Company recorded a deferred tax expense of $1.8 million and $2.3 million related to its U.S. operations during the three and six months ended June 30, 2026 ($0.4 million and $0.9 million for the three and six months ended June 30, 2025).

The effective income tax rate of 2.3% and 1.8% during the three and six months ended June 30, 2026 (three and six months ended June 30, 2025: 1.1% and 1.1%, respectively) is substantially lower than the enacted rate of 25.8% in the Netherlands as the Company recorded a valuation allowance against its net deferred tax assets in the Netherlands and a partial valuation allowance against its net deferred tax assets in France, among various other items which impacted the effective rate.

17

13Basic and diluted loss per share

Diluted loss per ordinary share is calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company incurred a loss in the three and six months ended June 30, 2026, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of diluted loss per share for the three and six months ended June 30, 2026. The ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that would be above the share price as of June 30, 2026 and June 30, 2025, respectively.

The potentially dilutive ordinary shares are summarized below:

Three months ended June 30, 

Six months ended June 30, 

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

Anti-dilutive ordinary share equivalents

Stock options under 2014 Plans

$

4,962,265

$

5,321,862

$

4,962,265

$

5,321,862

Non-vested RSUs and PSUs

2,536,549

2,442,969

2,536,549

2,442,969

Pre-Funded Warrants

526,316

526,316

ESPP

13,939

13,939

Total anti-dilutive ordinary share equivalents

8,039,069

7,764,831

8,039,069

7,764,831

14Commitments and contingencies

In the course of its business, the Company enters as a licensee into contracts with other parties regarding the development and marketing of its pipeline products. Among other payment obligations, the Company is obligated to pay royalties to the licensors based on future sales levels and milestone payments whenever specified development, regulatory and commercial milestones are met. As both future sales levels and the timing and achievement of milestones are uncertain, the financial effect of these agreements cannot be reliably estimated. The Company also has obligations to make future payments that become due and payable upon the collection of milestone payments from CSL Behring. The achievement and timing of these milestones are not fixed or determinable.

Legal Proceedings

On February 10, 2026, a class action complaint captioned Christopher Scocco v. uniQure N.V., et al., Case No. 1:26-cv-01124, was filed against the Company, certain of its executive officers and another party (collectively, “Defendants”) in the United States District Court for the Southern District of New York. The complaint purported to assert claims pursuant to Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and Rule 10b-5 promulgated thereunder, on behalf of a putative class of investors who purchased or otherwise acquired the Company’s ordinary shares between September 24, 2025 and October 31, 2025 (the “putative Class Period”). The plaintiff sought to recover damages allegedly caused by purported false and misleading statements and omissions with respect to the Company’s Phase I/II study of AMT-130 and the timing of the potential Biologics License Application filing for AMT-130.

On April 13, 2026, the court appointed the Oklahoma Firefighters Pension and Retirement System as lead plaintiff (the “Lead Plaintiff”).

On July 15, 2026, the Lead Plaintiff filed an amended complaint. Like the earlier-filed complaint, the amended complaint purports to assert claims pursuant to Sections 10(b) and 20(a) of the Exchange Act and Rule 10b-5, on behalf of a putative class of investors who purchased or otherwise acquired the Company’s ordinary shares during the putative Class Period. Lead Plaintiff seeks unspecified damages allegedly caused by purported false and misleading statements and omissions with respect to the import and viability of data from the Company’s Phase I/II study of AMT-130 and available pathways to regulatory approval. Defendants’ motion to dismiss the amended complaint is currently due September 14, 2026. Management intends to vigorously defend against the claims in this action.

At each reporting date, the Company evaluates whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of the authoritative guidance that addresses accounting for contingencies. The Company has not recorded any liability for any portion of this matter because the Company believes that liability is not probable and reasonably estimable at this time.

18

15Subsequent events

In July 2026, subsequent to the balance sheet date, the Company entered into an amendment to its loan facility with Hercules Capital, Inc. (as amended, the “2026 Amended Facility”). The amendment extended the period during which the Company may draw the $100.0 million term loan tranche from June 15, 2027 to September 30, 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility remained unchanged.

19

Item 2.Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion of our results of operations and financial condition should be read in conjunction with our unaudited consolidated financial statements and the accompanying notes thereto and other disclosures included in this Quarterly Report on Form 10-Q, including the disclosures under Part II, Item 1A “Risk Factors,” and our audited financial information and the notes thereto included in our Annual Report on Form 10-K (the “Annual Report”). Our unaudited consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States (“U.S. GAAP”) and unless otherwise indicated are presented in United States (“U.S.”) dollars.

Overview

We are a leader in the field of gene therapy, seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. We are advancing a focused pipeline of innovative gene therapies, including our clinical candidates for the treatment of Huntington’s disease, refractory mesial temporal lobe epilepsy (“MTLE”), and Fabry disease.

Business Developments

Financing

In June 2026, we received net proceeds of $242.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by us, through a follow-on public offering of 5.7 million ordinary shares, at a public offering price of $45.50 per ordinary share.

Hercules Loan Amendment

In July 2026, we entered into an amendment to the $175.0 million senior secured term loan facility (the “2026 Amended Facility”) with Hercules Capital, Inc. (“Hercules”). The 2026 Amended Facility, among other things, extends the period we can draw the $100.0 million term loan tranche from June 2027 to September 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility otherwise remain unchanged.

Recent Product Candidate Developments

Huntington’s disease program (AMT-130)

AMT-130 is our novel gene therapy candidate for the treatment of Huntington’s disease, which utilizes our proprietary, gene-silencing miQURE® platform and incorporates a miRNA, specifically designed to silence the huntingtin gene and the potentially highly toxic exon 1 protein fragment.

We are currently conducting Phase I/II clinical trials of AMT-130 in the U.S. and Europe. We completed the enrollment of all 26 patients in the first two cohorts of our U.S. study in March 2022 and the enrollment of 13 patients in the two cohorts of our European study in June 2023. In 2025, we completed enrollment of all 12 patients in the third cohort, and we treated six patients with the high-dose of AMT-130 in a fourth cohort to evaluate the safety and efficacy of AMT-130 in patients with lower baseline striatal volumes compared to previous cohorts in the U.S. Phase I/II study.

Data from Phase I/II Clinical Studies

In September 2025, we announced positive topline data from the three-year analysis of cohorts one and two of the ongoing Phase I/II studies of AMT-130 for the treatment of Huntington’s disease. We analyzed clinical outcomes for 29 patients treated with AMT-130 (n=17 high-dose; n=12 low-dose) of which 12 patients per dose group had attained 36 months of follow-up and were evaluated at that time point. Outcomes for each dose group were compared to a propensity score-matched external control drawn from the Enroll-HD natural history data set (n=940 for high-dose; n=626 for low-dose).

Topline 36-month efficacy results for patients receiving high-dose AMT-130 were as follows (data cutoff as of June 30, 2025):

20

A statistically significant 75% slowing of disease progression as measured by composite Unified Huntington’s Disease Rating Scale (“cUHDRS”) (p=0.003), which met the primary endpoint of the study. Treated patients had a mean change in cUHDRS from baseline of -0.38 compared to a change of -1.52 for patients in the propensity score-matched external control.
A statistically significant 60% slowing of disease progression as measured by Total Function Capacity (“TFC”) (p=0.033), which met a key secondary endpoint of the study. Treated patients had a mean change in TFC from baseline of -0.36 compared to a change of -0.88 for patients in the propensity score-matched external control.
Favorable trends in other secondary endpoint measures of motor and cognitive function, including Symbol Digit Modalities Test (“SDMT”), Stroop Word Reading Test (“SWRT”) and Total Motor Score (“TMS”).
oAn 88% slowing of disease progression as measured by SDMT (p=0.057), with a mean change in SDMT from baseline of -0.44 compared to a change of -3.73 for patients in the propensity score-matched external control.
oA 113% slowing of disease progression as measured by SWRT (nominal p=0.002), with a mean change in SWRT from baseline of 0.88 compared to a change of -6.98 for patients in the propensity score-matched external control.
oA 59% slowing of disease progression as measured by TMS (nominal p=0.174), with a mean change in TMS from baseline of 2.01 compared to a change of 4.88 for patients in the propensity score-matched external control.

A mean reduction from baseline in cerebrospinal neurofilament light protein (“CSF NfL”) of -8.2% was observed at 36 months in the high-dose of AMT-130 of the Phase I/II studies. CSF NfL is a well-characterized, supportive biomarker of neurodegeneration. Elevation in CSF NfL has been shown to be strongly associated with greater clinical severity of Huntington’s disease.

We believe that the consistently favorable results in functional, motor and cognitive endpoints at 36 months observed in the high-dose group, compared to the variable trends observed in the low-dose group, reflect a dose-dependent response to AMT-130.

Various other supportive analyses of the results from the AMT-130 high-dose treatment group, including those using a propensity score-weighted external control and comparisons to the TRACK-HD and PREDICT-HD datasets, were consistent with the primary analysis.

AMT-130 was generally well-tolerated in the Phase I/II studies, with a manageable safety profile at both doses. There have been five drug-related serious adverse events (“SAEs”) reported across all cohorts, and the most common adverse events in the treatment groups were related to the administration procedure.

Regulatory Update

From November 2024 through April 2025, we held three Type B meetings with the U.S. Food and Drug Administration (the “FDA”). As part of these interactions, the FDA agreed that data from the ongoing Phase I/II studies, compared to a natural history external control, may serve as the primary basis of a Biologics License Application (“BLA”) submission under the FDA’s accelerated approval pathway. The FDA also agreed that cUHDRS may be used as an intermediate clinical endpoint and reductions in CSF NfL may serve as supportive evidence of therapeutic benefit in the application for such accelerated approval.

In October 2025, we met with the FDA at a pre-BLA meeting to discuss the application for AMT-130. In December 2025, we announced that in the final meeting minutes, the FDA conveyed that data submitted from the Phase I/II studies of AMT-130 were currently unlikely to provide the primary evidence to support a BLA submission.

21

In January 2026, we met with the FDA at a Type A meeting to discuss AMT-130. In March 2026, following receipt of the final meeting minutes from the Type A meeting, we announced that the FDA stated that it could not agree that data from the Phase I/II studies, compared to an external control, were sufficient to provide the primary evidence of effectiveness required to support a marketing application for AMT-130. The FDA strongly recommended we conduct a prospective, randomized, double-blind, sham surgery-controlled study. 

In March 2026, we held a successful pre-submission meeting with the United Kingdom’s (“UK”) Medicines and Healthcare products Regulatory Agency (“MHRA”) regarding AMT-130, and the regulatory submission is progressing as planned for the third quarter of 2026.

In June 2026, we held a Type B meeting with the FDA. Official meeting minutes received in July 2026 confirmed that we and the FDA reached alignment that a BLA submission under the accelerated approval pathway for AMT-130, based on the existing clinical data, is reasonable. In addition, the FDA seeks to align on the confirmatory study design prior to the BLA submission, including consideration of a randomized standard-of-care control design instead of a sham procedure. The FDA also stated that, in accordance with the FDA’s draft public guidance for accelerated approvals, the confirmatory study should be feasible to conduct within a reasonable timeline and be well underway, and potentially fully enrolled, at the time of accelerated approval. Discussions with the FDA to align on the confirmatory study design and analysis are underway, and we expect to submit a BLA in the third quarter of 2026.

Temporal lobe epilepsy program (AMT-260)

We are conducting a Phase I/IIa clinical trial, GenTLE, of AMT-260 for the treatment of MTLE in the U.S. GenTLE is a multicenter, open-label trial with two dosing cohorts of at least six patients each to assess safety, tolerability, and initial efficacy of AMT-260 in patients with refractory MTLE.

In September 2025, we completed enrollment of the first three patients in the first cohort administering AMT-260 to patients with lesions in the non-dominant hemisphere of the brain. Following a review by the independent data monitoring committee (“IDMC”), we expanded the first cohort into MTLE in the dominant hemisphere and initiated a second cohort. We completed enrollment of six patients into the first cohort in 2025. We also initiated enrollment of a second cohort in 2025.

In June 2026, we announced preliminary data on the first cohort in GenTLE. As of the May 29, 2026 data cutoff date, three of six patients in the first, low-dose cohort (1x1012 gc/mL) achieved meaningful reductions in disabling seizures during months four through six of follow-up, ranging from a 79% to 100% decline from baseline. The remaining three patients in the low-dose cohort experienced variable changes in disabling seizures during months four through six of follow-up, ranging from a 33% decrease to a 36% increase compared to baseline. As of the June 19, 2026, there have been no SAEs related to AMT-260 or the surgical procedure reported. All reported adverse events in the low dose cohort were classified as mild or moderate in severity, with the most common adverse event being headache (N=2). No immunosuppression was required.

Fabry disease program (AMT-191)

We are conducting a Phase I/II clinical trial of AMT-191 for the treatment of Fabry disease. The multicenter, open-label clinical trial consists of three dose-ranging cohorts of three or more patients each to assess safety, tolerability, and efficacy of AMT-191 in patients with Fabry disease.

In June 2026, we presented updated preliminary data from the Phase I/II study of AMT-191 for Fabry disease. The data, based on a March 15, 2026 data cutoff date, included patient follow-up ranging from three months to more than 18 months and consisted of the following:

Dose-dependent elevations were observed across 11 patients in three dose levels with α-Gal A activity ranging from 1.0- to 16.2-fold above mean normal range (1.38-8.66 nmol; mean normal of 3.57 nmol) at the lowest dose, 14.5- to 229.6-fold at the mid dose, and 58.7- to 143.6-fold at the highest dose.
All 11 dosed patients were withdrawn from enzyme replacement therapy (“ERT”).
Plasma lyso-Gb3 levels were stable post-dose across all dose cohorts, regardless of ERT status through the cutoff date.

22

AMT-191 continued to show a manageable safety profile. No SAEs related to AMT-191 were observed at the 4x1013 gc/kg (“mid-dose”) and 2x1013 gc/kg (“low-dose”) doses. No additional SAEs were observed at the 6x1013 gc/kg (“high-dose”) dose beyond those previously reported in September 2025 in two patients.

Per protocol, additional dosing in the mid- and high-dose cohorts has been paused pending further evaluation following asymptomatic Grade 3 liver enzyme elevations observed in two patients in the mid-dose cohort, which were confirmed dose-limiting toxicity. These elevations resolved as of the end of May 2026 following a course of immunosuppression as per the study protocol.

Financial Overview

Key components of our results of operations include the following:

Three months ended June 30, 

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

(in thousands)

(in thousands)

Total revenues

$

5,841

$

5,262

$

9,403

$

6,829

Cost of license revenues

(350)

(656)

(569)

(853)

Research and development expenses

(33,964)

(35,383)

(63,140)

(71,523)

Selling, general and administrative expenses

(17,367)

(13,500)

(37,435)

(24,408)

Net loss

(81,059)

(37,719)

(134,594)

(81,356)

As of June 30, 2026 and December 31, 2025, we had cash and cash equivalents and investment securities of $810.3 million and $622.5 million, respectively. We had a net loss of $81.1 million and $134.6 million in the three and six months ended June 30, 2026, compared to a net loss of $37.7 million and $81.4 million for the same periods in 2025. As of June 30, 2026 and December 31, 2025, we had accumulated deficits of $1,463.5 million and $1,328.9 million, respectively. See “Results of Operations” below for a discussion of the detailed components and analysis of the amounts above.

Critical Accounting Policies and Estimates

In preparing our unaudited consolidated financial statements in accordance with U.S. GAAP and pursuant to the rules and regulations promulgated by the Securities and Exchange Commission (the “SEC”) we make assumptions, judgments and estimates that can have a significant impact on our net loss and affect the reported amounts of certain assets, liabilities, revenue and expenses, and related disclosures. We base our assumptions, judgments and estimates on historical experience and various other factors that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not clear from other sources. Actual results may differ from these estimates under different assumptions or conditions. In making estimates and judgments, management employs critical accounting policies. A summary of our critical accounting policies, as well as a discussion of our critical accounting estimates, are presented in our Annual Report. There were no material changes to our critical accounting policies during the six months ended June 30, 2026.

Research and development expenses

We expense research and development (“R&D”) expenses as incurred. R&D expenses include costs which relate to our primary activities of biopharmaceutical research and development. Our R&D expenses generally consist of costs incurred for the development of our target candidates, which include:

employee-related expenses, including salaries, benefits, travel and share-based compensation expense;
costs incurred for laboratory research, preclinical and nonclinical studies, clinical trials, statistical analysis and report writing, and regulatory compliance costs incurred with clinical research organizations and other third-party vendors;
costs incurred to conduct consistency and comparability studies;
costs incurred for the development and improvement of our manufacturing processes and methods;
costs associated with research activities for enabling technology platforms;
costs associated with the rendering of collaboration services;
payments related to identifiable intangible assets without an alternative future use;

23

payments to our licensors for milestones that have been achieved related to our product candidates;
facilities, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, insurance, and other supplies; and
changes in the fair value of liabilities recorded in relation to the acquisition of uniQure France SAS.

Our R&D expenses may vary substantially from period to period based on the timing of our research and development activities, including manufacturing campaigns, regulatory submissions, and enrollment of patients in clinical trials. The successful development of our product candidates is highly uncertain. Estimating the nature, timing, or cost of the development of any of our product candidates involves considerable judgment due to numerous risks and uncertainties associated with developing gene therapies, including the uncertainty of:

the scope, rate of progress and expense of our research and development activities;
clinical trial protocols, speed of enrollment and resulting data;
the effectiveness and safety of our product candidates; and
the timing of regulatory approvals.

A change in the outcome of any of these variables with respect to our product candidates that we may develop could mean a significant change in the expenses and timing associated with the development of such product candidates.

Selling, general and administrative expenses

Our selling, general and administrative expenses consist principally of employee, office, consulting, legal and other professional and administrative expenses. We incurred expenses associated with operating as a public company, including expenses for personnel, legal, accounting and audit fees, board of directors’ costs, directors’ and officers’ liability insurance premiums, Nasdaq listing fees, expenses related to investor relations and fees related to business development and maintaining our patent and license portfolio.

Other items, net

Our other income generally consists of payments received to subsidize our research and development efforts and income from the subleasing of our Amsterdam facility and our Lexington, MA research and development facility.

In 2024, as part of the divestment of our commercial manufacturing operations to Genezen Holdings Inc. and its subsidiary Genezen MA, Inc. (together “Genezen”), we entered into various service agreements, including a commercial supply agreement (the “Genezen CSA”). In April 2026, we entered into an agreement to terminate the Genezen CSA. Pursuant to the termination agreement, our obligation to supply HEMGENIX® and any minimum purchase commitments under the Genezen CSA terminate once contractually specified batches have been supplied.

Our other expenses consist of costs incurred under the Genezen CSA. These include costs related to the purchase of HEMGENIX® from Genezen, net of income from the sales of HEMGENIX® to CSL Behring LLC (“CSL Behring”), amortization of the intangible asset recorded with respect to the favorable supply terms under the Genezen CSA, and release of liabilities related to expected net losses associated with the remaining minimum purchase commitments under the Genezen CSA.

Additionally, other expenses also consist of expenses we incur in relation to our subleasing income.

24

Results of Operations

Comparison of the three months ended June 30, 2026 and 2025

The following table presents a comparison of our results of operations for the three months ended June 30, 2026 and 2025:

Three months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026 vs 2025

(in thousands)

License revenues

$

5,841

$

5,262

$

579

Total revenues

5,841

5,262

579

Operating expenses:

Cost of license revenues

(350)

(656)

306

Research and development expenses

(33,964)

(35,383)

1,419

Selling, general and administrative expenses

(17,367)

(13,500)

(3,867)

Total operating expenses

(51,681)

(49,539)

(2,142)

Other income

1,598

2,597

(999)

Other expense

(7,961)

(2,185)

(5,776)

Loss from operations

(52,203)

(43,865)

(8,338)

Non-operating (expense) / income, net

(27,015)

6,571

(33,586)

Net loss before income tax expense

$

(79,218)

$

(37,294)

$

(41,924)

Income tax expense

(1,841)

(425)

(1,416)

Net loss

$

(81,059)

$

(37,719)

$

(43,340)

License revenues

We recognize license revenues from CSL Behring related to royalty payments owed on HEMGENIX® sales, when earned. For the three months ended June 30, 2026 and 2025, we recognized $5.8 million and $5.3 million of license revenues, respectively.

R&D expense

R&D expenses for the three months ended June 30, 2026 were $34.0 million, compared to $35.4 million for the same period in 2025. Other research and development expenses are separately classified in the table below. These other expenses are not allocated to specific projects, as they are deployed across multiple projects under development.

Three months ended June 30, 

2026

2025

2026 vs 2025

(in thousands)

Huntington's disease (AMT-130)

$

6,280

$

10,517

$

(4,237)

Temporal lobe epilepsy (AMT-260)

4,168

1,955

2,213

Amyotrophic lateral sclerosis (AMT-162)

2,503

1,098

1,405

Fabry disease (AMT-191)

2,177

1,255

922

Programs in preclinical development and platform related expenses

1,883

405

1,478

Total direct research and development expenses

$

17,011

$

15,230

$

1,781

Employee and contractor-related expenses

9,111

9,523

(412)

Facility expenses

2,402

3,853

(1,451)

Share-based compensation expense

1,888

2,758

(870)

Information technology costs

966

594

372

Fair value changes related to contingent consideration

1,256

2,254

(998)

Other expenses

1,330

1,171

159

Total other research and development expenses

$

16,953

$

20,153

$

(3,200)

Total research and development expenses

$

33,964

$

35,383

$

(1,419)

25

Direct research and development expenses

Huntington’s disease (AMT-130)

In the three months ended June 30, 2026 and 2025, we incurred costs related to the development of AMT-130 of $6.3 million and $10.5 million respectively. The decrease of $4.2 million was primarily related to lower manufacturing process validation costs, which were $0.8 million in the current year period, compared to $4.0 million in the prior year period. Additionally, clinical trials costs decreased in the current year period, partially offset by higher regulatory costs associated with the preparation of BLA and Marketing Authorization Application (“MAA”) submissions for AMT-130 in the United States and the United Kingdom, respectively.

Temporal lobe epilepsy (AMT-260)

In the three months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-260 of $4.2 million and $2.0 million, respectively. The current year period included $3.7 million of clinical expenses and $0.3 million of CMC expenses, respectively, compared to $1.7 million and $0.2 million, respectively, in the prior year period.

Amyotrophic Lateral Sclerosis caused by mutations in SOD1 (AMT-162)

In the three months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-162 of $2.5 million and $1.1 million, respectively. These costs were primarily related to our Phase I/II clinical trial.

Fabry disease (AMT-191)

In the three months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-191 of $2.2 million and $1.3 million, respectively. These costs were primarily related to our Phase I/II trial.

Preclinical programs & platform development

In the three months ended June 30, 2026 and June 30, 2025, we incurred costs related to research and technology projects of $1.9 million and $0.4 million, respectively.

Other research & development expenses

We incurred $9.1 million in personnel and contractor-related expenses in the three months ended June 30, 2026, compared to $9.5 million for the same period in 2025;
We incurred $2.4 million in operating and depreciation expenses related to our leased facilities in Amsterdam and Lexington, Massachusetts in the three months ended June 30, 2026 compared to $3.9 million in the same period in 2025;
We incurred $1.9 million in share-based compensation expenses in the three months ended June 30, 2026, compared to $2.8 million for the same period in 2025. The decrease of $0.9 million was primarily driven by lower costs related to performance stock units during the current year period; and
We incurred a $1.3 million loss related to an increase in the fair value of contingent consideration associated with the acquisition of uniQure France SAS in the three months ended June 30, 2026, compared to a $2.3 million loss for the same period in 2025. The $1.0 million favorable change reflects that the prior period included an adjustment to the expected timing of achieving future milestones that did not recur in the current year period.

26

Selling, general and administrative expenses

Selling, general and administrative expenses for the three months ended June 30, 2026 were $17.4 million, compared to $13.5 million for the same period in 2025.

Three months ended June 30, 

2026

2025

2026 vs 2025

(in thousands)

Employee and contractor-related expenses

$

8,878

$

5,397

$

3,481

Share-based compensation expense

3,128

2,326

802

Professional fees

1,592

3,428

(1,836)

Intellectual property fees

983

281

702

Depreciation and facility costs

508

578

(70)

Information technology costs

389

193

196

Other expenses

1,889

1,297

592

Total selling, general and administrative expenses

$

17,367

$

13,500

$

3,867

We incurred $8.9 million in personnel and contractor-related expenses in the three months ended June 30, 2026, compared to $5.4 million in the same period in 2025. The $3.5 million increase was primarily driven by of a higher headcount following employee recruitment in the second half of 2025 to support the potential commercial launches of AMT-130;
We incurred $3.1 million in share-based compensation expenses in the three months ended June 30, 2026, compared to $2.3 million in the same period in 2025. The $0.8 million increase was primarily driven by the higher  fair value of awards outstanding during the current year period, in comparison with the prior period;
We incurred $1.6 million in professional fees in the three months ended June 30, 2026 compared to $3.4 million in the same period in 2025. The $1.8 million decrease was primarily a result of lower costs in connection with the potential commercial launches of AMT-130; and
We incurred $1.9 million in other expenses in the three months ended June 30, 2026, compared to $1.3 million in the same period in 2025.

Other income and expense

Three months ended June 30, 

2026

2025

2026 vs 2025

(in thousands)

Research and development grants from Dutch authorities

$

1,164

$

1,392

$

(228)

Sublease income, net

337

347

(10)

Supply of HEMGENIX® to CSL Behring

(7,695)

(1,731)

(5,964)

Other income, net

(169)

404

(573)

Total other items, net

$

(6,363)

$

412

$

(6,775)

In April 2026, we entered into an agreement to terminate the Genezen CSA. In connection with the termination, we recorded a write-down of $5.9 million related to the favorable supply intangible asset within Other expense.

27

Other non-operating items, net

Our other non-operating items, net, for the three months ended June 30, 2026 and June 30, 2025 were as follows:

Three months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026 vs 2025

(in thousands)

Interest income

$

5,051

$

3,524

$

1,527

Interest expense - Royalty Financing Agreement

(12,963)

(13,770)

807

Interest expense - Hercules loan facility

(1,403)

(1,821)

418

Foreign currency (losses) / gains, net

(1,730)

18,638

(20,368)

Changes in fair value of liability related to pre-funded warrants

(15,970)

(15,970)

Total non-operating items, net

$

(27,015)

$

6,571

$

(33,586)

We recognize interest income associated with our cash and cash equivalents and investment securities. We recognized $5.1 million in interest income in the three months ended June 30, 2026, compared to $3.5 million in the same period in 2025. The $1.5 million increase was primarily due to higher average balances of our investment securities held during the current year period, compared to the prior year period.

In May 2023, uniQure biopharma B.V. entered into an agreement (the “Royalty Financing Agreement”) with HemB SPV, L.P. to sell certain current and future royalties due to uniQure biopharma B.V. from CSL Behring from the net sales of HEMGENIX® pursuant to the CSL Behring Agreement. We recognized non-cash interest expenses related to the Royalty Financing Agreement of $13.0 million and $13.8 million in the three months ended June 30, 2026 and 2025, respectively.

We recognized interest expense related to the Hercules loan facility of $1.4 million and $1.8 million in the three months ended June 30, 2026 and June 30, 2025, respectively. The $0.4 million decrease was primarily due to more favorable terms following the amendment of the facility in September 2025, as well as a decrease in market interest rates.

We conduct transactions and hold monetary assets and liabilities denominated in foreign currencies, principally the euro and the U.S. dollar. Monetary balances are remeasured at period-end exchange rates, and resulting foreign currency transaction gains and losses are recorded in the Unaudited Consolidated Statements of Operations and Comprehensive Loss as incurred.

We recognized a net foreign currency loss of $1.7 million during the three months ended June 30, 2026, compared to a net gain of $18.6 million during the same period in 2025.  The foreign currency movements relate to our Hercules loan facility, the Royalty Financing Agreement, cash and cash equivalents, investment securities, and intercompany loans within the uniQure group.

In connection with our September 2025 follow-on public offering, we issued pre-funded warrants that are classified as a liability and measured at fair value each reporting period. We recognized a $16.0 million loss in the three months ended June 30, 2026, reflecting an increase in the fair value of this liability, compared to nil for the same period in 2025.

Income tax expense

We recognized $1.8 million of deferred tax expense in the three months ended June 30, 2026, and $0.4 million of deferred tax expense for the same period in 2025.

28

Results of Operations

Comparison of the six months ended June 30, 2026 and 2025

The following table presents a comparison of our results of operations for the six months ended June 30, 2026 and 2025:

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026 vs 2025

(in thousands)

Total revenues

$

9,403

$

6,829

$

2,574

Operating expenses:

Cost of license revenues

(569)

(853)

284

Research and development expenses

(63,140)

(71,523)

8,383

Selling, general and administrative expenses

(37,435)

(24,408)

(13,027)

Total operating expenses

(101,144)

(96,784)

(4,360)

Other income

3,230

10,903

(7,673)

Other expense

(9,412)

(4,144)

(5,268)

Loss from operations

(97,923)

(83,196)

(14,727)

Non-operating (expense) / income, net

(34,342)

2,761

(37,103)

Loss before income tax expense

$

(132,265)

$

(80,435)

(51,830)

Income tax expense

(2,329)

(921)

(1,408)

Net loss

$

(134,594)

$

(81,356)

$

(53,238)

License revenues

We recognize license revenues from CSL Behring related to royalty payments owed on HEMGENIX® sales, when earned. For the six months ended June 30, 2026 and 2025, we recognized $9.4 million and $6.8 million of license revenues, respectively.

R&D expense

R&D expenses for the six months ended June 30, 2026 were $63.1 million, compared to $71.5 million for the same period in 2025. Other research and development expenses are separately classified in the table below. These other expenses are not allocated to specific projects, as they are deployed across multiple projects under development.

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026 vs 2025

(in thousands)

Huntington's disease (AMT-130)

$

14,260

$

18,747

$

(4,487)

Temporal lobe epilepsy (AMT-260)

6,995

4,030

2,965

Fabry disease (AMT-191)

3,716

3,442

274

Amyotrophic lateral sclerosis (AMT-162)

3,397

2,929

468

Programs in preclinical development and platform related expenses

3,017

1,685

1,332

Total direct research and development expenses

$

31,385

$

30,833

$

552

Employee and contractor-related expenses

18,171

19,682

(1,511)

Facility expenses

6,021

8,403

(2,382)

Share-based compensation expense

3,865

5,221

(1,356)

Information technology costs

2,056

1,276

780

Fair value changes related to contingent consideration

(82)

3,470

(3,552)

Other expenses

1,724

2,638

(914)

Total other research and development expenses

$

31,755

$

40,690

$

(8,935)

Total research and development expenses

$

63,140

$

71,523

$

(8,383)

29

Direct research and development expenses

Huntington’s disease (AMT-130)

In the six months ended June 30, 2026 and 2025, we incurred costs related to the development of AMT-130 of $14.3 million and $18.7 million respectively. The decrease of $4.5 million was primarily driven by lower costs related to clinical trials of $9.0 million in the current period, compared to $11.2 million in the prior year period. Additionally, manufacturing process validation costs were decreased in the current year period, partially offset by higher regulatory costs associated with the preparation of BLA and MAA submissions for AMT-130 in the United States and the United Kingdom, respectively.

Temporal lobe epilepsy (AMT-260)

In the six months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-260 of $7.0 million and $4.0 million, respectively. The current period included costs of $6.3 million related to clinical trials and $0.5 million related to CMC development, compared to $3.3 million and $0.7 million, respectively, in the prior year period.

Fabry disease (AMT-191)

In the six months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-191 of $3.7 million and $3.4 million, respectively. These costs primarily related to the Phase I/II trial.

Amyotrophic Lateral Sclerosis caused by mutations in SOD1 (AMT-162)

In the six months ended June 30, 2026 and June 30, 2025, we incurred costs related to the development of AMT-162 of $3.4 million and $2.9 million, respectively. These costs primarily related to the Phase I/II trial.

Preclinical programs & platform development

In the six months ended June 30, 2026 and June 30, 2025, we incurred costs related to research and technology projects of $3.0 million and $1.7 million, respectively.

Other research & development expenses

We incurred $18.2 million in personnel and contractor-related expenses in the six months ended June 30, 2026, compared to $19.7 million for the same period in 2025. The decrease of $1.5 million was primarily due to lower personnel-related expenses in the current year period;
We incurred $6.0 million in operating and depreciation expenses related to our leased facilities in Amsterdam and Lexington, Massachusetts in the six months ended June 30, 2026 compared to $8.4 million in the same period in 2025. The decrease of $2.4 million was primarily driven by a revision to the estimated useful lives of certain assets, resulting in higher depreciation recognized during the prior year period;
We incurred $3.9 million in share-based compensation expenses in the six months ended June 30, 2026, compared to $5.2 million for the same period in 2025. The decrease of $1.3 million was primarily driven by lower costs related to performance stock units during the current year period;
We incurred a $0.1 million gain related to a decrease in the fair value of contingent consideration associated with the acquisition of uniQure France SAS in the six months ended June 30, 2026, compared to a $3.5 million loss for the same period in 2025. The $3.6 million favorable change was primarily driven by movements in the discount rate and the timing of future milestone achievements; and
We incurred $1.7 million of other expenses for the six months ended June 30, 2026, compared to $2.6 million for the same period in 2025.

Selling, general and administrative expenses

Selling, general and administrative expenses for the six months ended June 30, 2026 were $37.4 million, compared to $24.4 million for the same period in 2025.

30

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

  ​ ​ ​

2026 vs 2025

(in thousands)

Employee and contractor-related expenses

$

18,733

$

10,882

$

7,851

Share-based compensation expense

6,241

4,273

1,968

Professional fees

5,247

5,331

(84)

Intellectual property fees

1,855

564

1,291

Information technology costs

909

474

435

Depreciation and facility costs

845

958

(113)

Other expenses

3,605

1,926

1,679

Total selling, general and administrative expenses

$

37,435

$

24,408

$

13,027

We incurred $18.7 million in personnel and contractor-related expenses in the six months ended June 30, 2026, compared to $10.9 million in the same period in 2025. The $7.8 million increase was primarily driven by higher headcount following employee recruitment in the second half of 2025 to support the potential commercial launches of AMT-130;
We incurred $5.2 million in professional fees in the six months ended June 30, 2026 compared to $5.3 million in the same period in 2025;
We incurred $6.2 million in share-based compensation expenses in the six months ended June 30, 2026, compared to $4.3 million in the same period in 2025. The $1.9 million increase was primarily driven by the higher fair value of awards outstanding during the current year period, in comparison with the prior period;
We incurred $1.9 million in intellectual property fees in the six months ended June 30, 2026 compared to $0.6 million in the same period in 2025. The $1.3 million increase was primarily driven by higher registration and professional fees; and
We incurred $3.6 million in other expenses in the six months ended June 30, 2026, compared to $1.9 million in the same period in 2025.

Other income and expense

Six months ended June 30, 

2026

2025

2026 vs 2025

(in thousands)

Research and development grants from Dutch authorities

2,122

3,111

(989)

Sublease income, net

606

371

235

Sale of critical reagents to Genezen

  ​ ​ ​

$

  ​ ​ ​

$

6,000

  ​ ​ ​

$

(6,000)

Supply of HEMGENIX® to CSL Behring

(8,880)

(3,256)

(5,624)

Other income, net

(30)

533

(563)

Total other items, net

$

(6,182)

$

6,759

$

(12,941)

In April 2026, we entered into an agreement to terminate the Genezen CSA. In connection with the termination, we recorded a write-down of $5.9 million related to the favorable supply intangible asset in Other expense.

31

Other non-operating items, net

Our other non-operating items, net, for the six months ended June 30, 2026 and June 30, 2025 were as follows:

Six months ended June 30, 

2026

2025

2026 vs 2025

(in thousands)

Interest income

  ​ ​ ​

$

10,280

  ​ ​ ​

$

7,651

  ​ ​ ​

$

2,629

Interest expense - Royalty Financing Agreement

(25,584)

(27,079)

1,495

Interest expense - Hercules loan facility

(2,814)

(3,621)

807

Foreign currency (losses) / gains, net

(4,024)

25,810

(29,834)

Changes in fair value of liability related to pre-funded warrants

(12,201)

(12,201)

Total Other non-operating items, net

$

(34,342)

$

2,761

$

(37,103)

We recognize interest income associated with our cash and cash equivalents and investment securities. We recognized $10.3 million in interest income in the six months ended June 30, 2026, compared to $7.7 million in the same period in 2025. The $2.6 million increase was primarily due to higher average balances of investment securities held during the current year period, compared to the prior year period.

We recognized interest expense related to the Hercules loan facility of $2.8 million in the six months ended June 30, 2026, compared to $3.6 million in the same period in 2025. The $0.8 million decrease was primarily due to more favorable terms following the amendment of the facility in September 2025, as well as a decrease in market interest rates.

We recognized a net foreign currency loss of $4.0 million in the six months ended June 30, 2026, compared to a net gain of $25.8 million in the same period in 2025. The foreign currency movements related to our borrowings from Hercules, the Royalty Financing Agreement, cash and cash equivalents, investment securities, and intercompany loans within the uniQure group.

Income tax expense

We recognized $2.3 million of deferred tax expense in the six months ended June 30, 2026, compared to $0.9 million in the same period in 2025.

32

Financial Position, Liquidity and Capital Resources

As of June 30, 2026, we had cash and cash equivalents, restricted cash and investment securities of $811.9 million. We believe these resources will be sufficient to fund our projected operating expenses into 2030, including costs associated with the commercial launches and confirmatory study of AMT-130, ongoing clinical trials of AMT-130, AMT-191 and AMT-260, and potential investments to advance certain pipeline candidates into late stage development. The amount and timing of our actual expenditures may vary significantly depending on the commencement and design of any new clinical studies that we may conduct. We have based our estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect, and as such, we may require additional funding.

This includes up to $100.0 million in additional availability under our Hercules senior secured term loan facility, which becomes accessible upon BLA approval for AMT-130 prior to September 30, 2027, subject to confirmatory trial requirements remaining on track. Additional funding could also include a combination of public equity offerings, collaborations, strategic alliances, licensing arrangements or marketing and distribution arrangements, which may not be possible. If adequate funds are not available to us on acceptable terms when we need them, we may be unable to pursue further development of our clinical product candidates.

Our current material cash requirements include the following contractual and other obligations:

Debt

As of June 30, 2026, we had an outstanding loan amount owed to Hercules for an aggregate principal amount of $50.0 million. The loan has an interest-only period until October 1, 2028 and we are contractually required to repay the $50.0 million in equal installments between October 1, 2028 and October 1, 2030. The interest-only period will be extended to October 1, 2029 if the BLA for AMT-130 is approved prior to October 1, 2028. The interest-only period will be further extended to October 1, 2030 if certain commercial milestones are met prior to March 31, 2029. Future contractual interest payments (assuming repayments commence on October 1, 2028) associated with the loan are $19.5 million, with $5.4 million payable within the next 12 months.

Leases

We have entered into lease arrangements for facilities, including corporate, laboratories and office space. As of June 30, 2026, we had fixed lease payment obligations of $22.9 million, with $5.2 million payable within the next 12 months. Following the closing of the Lexington Transaction, we assigned our lease for our prior manufacturing facility in Lexington, MA to Genezen. As of June 30, 2026, we remain obligated under a guarantee of lease payments of $14.0 million, with the maximum potential exposure under the guarantee decreasing over the remaining lease term through May 2029.

Commitments related to uniQure France SAS acquisition (nominal amounts)

In connection with our acquisition of uniQure France SAS, we entered into commitments to make payments to the former shareholders upon the achievement of certain contractually defined milestones. The commitments include payments related to post-acquisition services that we agreed to as part of the transaction. As of June 30, 2026, our remaining commitment amounts include EUR 160.0 million ($182.3 million) in potential milestone payments associated with Phase III development and the approval of AMT-260 in the U.S. and European Union. The timing of achieving these milestones and consequently the timing of payments, as well as whether the milestones will be achieved at all, is generally uncertain. These payments are owed in euro and have been translated at the foreign exchange rate as of June 30, 2026 of $1.14/€1.00. As of June 30, 2026, we expect these obligations will become payable between 2030 and 2034. If and when due, up to 25% of the milestone payments can be settled with our ordinary shares.

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Commitments related to licensors and financial advisors

We have obligations to make future payments to third parties that become due and payable on the achievement of certain development, regulatory and commercial milestones (such as the start of a clinical trial, filing of a BLA, approval by the FDA or product launch) or as a result of collecting payments related to our sale of the exclusive global rights of HEMGENIX® to CSL Behring. We also owe payments to a financial advisor related to certain payments we will collect under the CSL Behring Agreement.

The table below summarizes our consolidated cash flow data for the six months ended June 30, 2026 and 2025:

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Cash, cash equivalents and restricted cash at the beginning of the period

$

81,801

$

160,329

Net cash used in operating activities

(66,819)

(83,995)

Net cash generated from investing activities

151,819

93,172

Net cash generated from financing activities

249,666

80,714

Foreign exchange impact

(1,906)

5,052

Cash, cash equivalents and restricted cash at the end of period

$

414,561

$

255,272

We have previously incurred losses and cumulative negative cash flows from operations since our business was founded by our predecessor entity AMT Therapeutics Holding N.V. in 1998, with the exception of generating income in 2021 after receiving the upfront payment upon closing of the CSL Behring Agreement. We continued to incur losses in the current period. We recorded a net loss of $81.1 million and $134.6 million in the three and six months ended June 30, 2026, compared to a net loss of $37.7 million and $81.4 million during the same period in 2025. As of June 30, 2026, we had an accumulated deficit of $1,463.5 million.

Sources of liquidity

From our first institutional venture capital financing in 2006 through to the current period, we have funded our operations primarily through private and public placements of equity securities, debt securities, pre-funded warrants, and payments from our collaboration partners, as well as $370.1 million through the sale of a portion of royalties due from our collaboration partner CSL Behring in 2023. Between July 2021 and July 2023, we collected $617.4 million from CSL Behring as a result of the sale of HEMGENIX® to CSL Behring and other milestones collected from CSL Behring, and we are eligible to receive additional milestone payments, as well as royalties (to the extent not owed to settle the liability from the Royalty Financing Agreement) on net sales of HEMGENIX®.

In June 2026, we received aggregate net proceeds of $242.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by us, following the completion of a follow-on public offering of 5.7 million ordinary shares at a public offering price of $45.50 per ordinary share.

We are subject to certain covenants under the senior secured term loan facility with Hercules and may become subject to covenants under any future indebtedness that could limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends, which could adversely impact our ability to conduct our business. In addition, our pledge of assets as collateral to secure our obligations under the senior secured term loan facility with Hercules may limit our ability to obtain debt financing.

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To the extent we need to finance our cash needs through equity offerings or debt financings, such financing may be subject to unfavorable terms including without limitation, the negotiation and execution of definitive documentation, as well as credit and debt market conditions, and we may not be able to obtain such financing on terms acceptable to us or at all. If financing is not available when needed, including through debt or equity financings, or is available only on unfavorable terms, we may be unable to meet our cash needs. If we raise additional funds through collaborations, strategic alliances or marketing, distribution, or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams or product candidates or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings when needed, we may be required to delay, limit, reduce or terminate our product development or future commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves, which could have a material adverse effect on our business, financial conditions, results of operations and cash flows.

Net cash used in operating activities

Net cash used in operating activities was $66.8 million for the six months ended June 30, 2026 and consisted of a net loss of $134.6 million, adjusted for non-cash items including depreciation and amortization expense of $7.9 million, amortization of the discount on investment securities of $7.9 million, share-based compensation expense of $10.1 million, $17.4 million of interest expense net of interest paid related the Royalty Financing Agreement, a change in deferred taxes of $2.3 million, changes in the fair value of contingent consideration of $0.1 million, changes in the fair value of the liability related to pre-funded warrants of $12.2 million and unrealized foreign exchange losses of $8.3 million. Net cash used in operating activities also included favorable changes in operating assets and liabilities of $20.0 million. There was a net decrease in accounts receivable, accrued income, prepaid expenses, and other current assets and receivables of $8.8 million. There was a net increase in accounts payable, accrued expenses, and operating leases of $11.1 million.

Net cash used in operating activities was $84.0 million for the six months ended June 30, 2025 and consisted of net loss of $81.4 million adjusted for non-cash items, including depreciation and amortization expense of $8.2 million, amortization of the discount on investment securities of $4.2 million, share-based compensation expense of $9.5 million, $20.6 million of interest expense net of interest paid related the Royalty Financing Agreement, a change in deferred taxes of $0.9 million, changes in the fair value of contingent consideration of $3.5 million, and unrealized foreign exchange gains of $25.2 million. Net cash used in operating activities also included unfavorable changes in operating assets and liabilities of $12.3 million. There was a net increase in accounts receivable, prepaid expenses, and other current assets and receivables of $6.8 million. There was a net decrease in accounts payable, accrued expenses, other liabilities, and operating leases of $5.6 million.

Net cash generated from investing activities

In the six months ended June 30, 2026, we generated $151.8 million from our investing activities compared to $93.2 million generated during the same period in 2025.

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Cash flows from investing activities

Proceeds from maturity of debt securities

$

384,981

$

213,763

Investment in debt securities

(232,550)

(120,205)

Capital expenditures

(612)

(386)

Net cash generated from investing activities

$

151,819

$

93,172

35

Net cash generated from financing activities

In the six months ended June 30, 2026, net cash generated from financing activities was $249.7 million, compared to net cash generated from financing activities of $80.7 million in the same period in 2025.

Six months ended June 30, 

  ​ ​ ​

2026

  ​ ​ ​

2025

(in thousands)

Cash flows from financing activities

Proceeds from follow-on public offering of ordinary shares, net of issuance costs

$

242,681

$

80,511

Proceeds from issuance of ordinary shares related to employee stock options and purchase plans

6,985

203

Net cash generated from financing activities

$

249,666

$

80,714

Funding requirements

Our future capital requirements will depend on many factors, including but not limited to:

activities to prepare for the potential commercialization of AMT-130 for Huntington’s disease;
investments required to support the MAAs of AMT-130 or generate confirmatory evidence in conjunction with obtaining accelerated approval;
investments in the late stage development of AMT-191 and AMT-260;
earnout payments we might owe the former shareholders of uniQure France SAS, which are subject to achieving specific development and regulatory milestones;
contractual milestone payments and royalties we might be owed in accordance with the CSL Behring Agreement;
the scope, timing, results, and costs of our current and planned clinical trials;
the scope, obligations and restrictions on our business related to our existing equity, debt or royalty monetization financings and underlying agreements;
the extent to which we acquire or in-license other businesses, products, product candidates or technologies;
the scope, timing, results and costs of preclinical development and laboratory testing of our additional product candidates;
the need for additional resources and related recruitment costs to support the preclinical and clinical development of our product candidates;
the need for any additional tests, studies, or trials beyond those originally anticipated to confirm the safety or efficacy of our product candidates and technologies;
the cost, timing and outcome of regulatory reviews associated with our product candidates;
our ability to enter into collaboration arrangements in the future; and
the costs and timing of preparing, filing, expanding, acquiring, licensing, maintaining, enforcing, and prosecuting patents and patent applications, as well as defending any intellectual property-related claims.

Item 3.Quantitative and Qualitative Disclosures about Market Risk

We are exposed to a variety of financial risks in the normal course of our business, including market risk (including currency, price, and interest rate risk), credit risk and liquidity risk. Our overall risk management program focuses on the preservation of capital and the unpredictability of financial markets and has sought to minimize potential adverse effects on our financial performance and position.

Our market risks and exposures to such market risks during the three months ended June 30, 2026, have not materially changed from our market risks and our exposure to market risk discussed in Part II, Item 7A of our Annual Report.

36

Item 4.Controls and Procedures

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our chief executive officer (“CEO”) and chief financial officer (“CFO”), evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”) as of June 30, 2026. Based on such evaluation, our CEO and CFO concluded that as of June 30, 2026, our disclosure controls and procedures were effective to ensure that information required to be disclosed by it in reports the Company files or submits under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the rules and forms of the SEC, and that such material information is accumulated and communicated to the Company’s management, including its Principal Executive Officer and Principal Financial Officer, to allow timely decisions regarding required disclosure. Because of the inherent limitations in all control systems, any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and management necessarily is required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Furthermore, the Company’s controls and procedures can be circumvented by the individual acts of some persons, by collusion of two or more people or by management override of such control, and misstatements due to error or fraud may occur and not be detected on a timely basis.

Changes in Internal Control over Financial Reporting

During the period covered by this Quarterly Report on Form 10-Q, there were no changes in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Part II – OTHER INFORMATION

Item 1.Legal Proceedings

On February 10, 2026, a class action complaint captioned Christopher Scocco v. uniQure N.V., et al., Case No. 1:26-cv-01124, was filed against us, certain of our executive officers and another party (collectively, “Defendants”) in the United States District Court for the Southern District of New York. The complaint purported to assert claims pursuant to Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and Rule 10b-5 promulgated thereunder, on behalf of a putative class of investors who purchased or otherwise acquired our ordinary shares between September 24, 2025 and October 31, 2025 (the “putative Class Period”). The plaintiff sought to recover damages allegedly caused by purported false and misleading statements and omissions with respect to our Phase I/II study of AMT-130 and the timing of the potential BLA filing for AMT-130.

On April 13, 2026, the court appointed the Oklahoma Firefighters Pension and Retirement System as lead plaintiff (the “Lead Plaintiff”).

On July 15, 2026, the Lead Plaintiff filed an amended complaint. Like the earlier-filed complaint, the amended complaint purports to assert claims pursuant to Sections 10(b) and 20(a) of the Exchange Act and Rule 10b-5, on behalf of a putative class of investors who purchased or otherwise acquired our ordinary shares during the putative Class Period. Lead Plaintiff seeks unspecified damages allegedly caused by purported false and misleading statements and omissions with respect to the import and viability of data from our Phase I/II study of AMT-130 and available pathways to regulatory approval. Defendants’ motion to dismiss the amended complaint is currently due September 14, 2026. Management intends to vigorously defend against the claims in this action.

At each reporting date, we evaluate whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of the authoritative guidance that addresses accounting for contingencies. We have not recorded any liability for any portion of this matter because we believe that liability is not probable and reasonably estimable at this time.

37

Item 1A.Risk Factors

For a discussion of our risks, please see “Item 1A. Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2025. The information presented below updates, and should be read in conjunction with, the risk factors disclosed in our Annual Report on Form 10-K for the year ended December 31, 2025. Except as presented below, there have been no material changes from the risk factors described in our Annual Report on Form 10-K for the year ended December 31, 2025.

We are dependent on the success of our lead clinical product candidate, AMT-130, for the treatment of Huntington’s disease. A failure of AMT-130 in clinical development, including inability to demonstrate sufficient safety or efficacy, or challenges associated with its regulatory approval, manufacturing or commercialization could adversely affect our business.

We have invested a significant portion of our development efforts and financial resources in the development of our lead clinical product candidate, AMT-130 for the treatment of Huntington’s disease.

In June 2026, we held a Type B meeting with the FDA. Official meeting minutes received in July 2026 confirmed that we and the FDA reached alignment that a BLA submission under the accelerated approval pathway for AMT-130, based on the existing clinical data, is reasonable. In addition, the FDA seeks to align on the confirmatory study design prior to the BLA submission, including consideration of a randomized standard-of-care control design instead of a sham procedure. The FDA also stated that, in accordance with the FDA’s draft public guidance for accelerated approvals, the confirmatory study should be feasible to conduct within a reasonable timeline and be well underway, and potentially fully enrolled, at the time of accelerated approval. We expect to submit a BLA in the third quarter of 2026. We can provide no assurance that we will align with the FDA on a confirmatory study design or that our BLA will be accepted for review or, if accepted, that our BLA will result in approval of AMT-130 in Huntington’s disease by the FDA, or that the FDA will agree that we have met the FDA’s requirements for our confirmatory study at the time of the BLA action date.

In March 2026, we held a successful pre-submission meeting with the UK MHRA, and the regulatory submission is progressing as planned for the third quarter of 2026. We can provide no assurance that any such submission will result in approval of AMT-130 in the UK.

There are numerous other factors that could impede or otherwise negatively impact our further development of AMT-130, including, but not limited to: our inability to reach agreement with the FDA on the design of a confirmatory study prior to a BLA submission; potential patient safety issues; our failure to demonstrate sufficient clinical efficacy or durability of response data to warrant further development or approval by the FDA, MHRA or any other regulatory authority; shifting regulatory standards for approval; our current beliefs regarding the further development of and approval pathway for AMT-130, which are based on our interpretation of communications and interactions with regulatory authorities to date, and the success of our efforts to address such communications and interactions; the results from future interim or topline data analyses and readouts from our ongoing Phase I/II trials, including as additional patient data becomes available; any requirement for additional studies to obtain approval, including a confirmatory study; our ability to fund and enroll a confirmatory study, including engaging sites that may be needed to enroll participants in a confirmatory study; the timing, cost and resources associated with our planned marketing applications; our ability to successfully commercialize AMT-130 should we choose to do so without a partner; challenges with potential development or commercial partners, should we choose to pursue further development or commercialization of AMT-130 with a partner; and our ability to fund the further development and commercialization of the AMT-130 program.

Any one or combination of these factors could force us to halt or discontinue the ongoing clinical trials of AMT-130 or related commercialization efforts or could prevent us from obtaining marketing approval within the predicted timeframes or at all. Certain of these risks are heightened in the context of drug development for rare diseases like Huntington’s disease and novel investigational products like gene therapies in which non-traditional study designs may be utilized to demonstrate efficacy and safety, including open-label studies, single arm studies, studies utilizing active comparators or natural history data, biomarkers or other forms of surrogate endpoints, which may be utilized due to the challenges inherent in designing and conducting clinical trials for severe diseases that progress slowly and that affect small patient populations.

38

The FDA has broad discretion with regard to licensure, including through the Accelerated Approval Program, and even if we believe that the Accelerated Approval Program is appropriate for AMT-130, the FDA may require additional studies and trials beyond those that we currently contemplate. Furthermore, even if the FDA reviews a BLA seeking approval, including accelerated approval, there can be no assurance that licensure will be granted on a timely basis, or at all. The FDA may disagree that the design of, or results from, our studies and statistical analysis plan (“SAP”) support accelerated approval. Additionally, the FDA may require us to conduct further studies or trials prior to granting licensure of any type, including by determining that licensure through the Accelerated Approval Program is not appropriate and that our clinical trials and SAP for AMT-130 may not be used to support licensure through the conventional pathway. We might not be able to fulfill the FDA’s requirements in a timely manner, which would cause delays, or licensure might not be granted because our submission is deemed incomplete by the FDA. Furthermore, the feedback or requests we receive from the FDA, or other non-U.S. regulatory authority, may be difficult or impossible to implement. There also can be no assurance that after subsequent FDA feedback we will continue to pursue licensure, including through the Accelerated Approval Program or otherwise. A failure to obtain licensure for AMT-130 could delay or prevent our ability to launch and commercialize AMT-130 in the U.S., could result in a longer time period to pursue licensure of our other clinical product candidates or increase the cost of development of our other clinical product candidates, and could significantly harm our financial position and competitive position in the marketplace.

We cannot be certain that AMT-130, or any of our clinical product candidates, will be successful in clinical trials or ultimately receive regulatory approval. If we were required, or if we chose, to discontinue development of AMT-130 or any other current or future product candidate, or if any of them were to fail to receive regulatory approval or achieve sufficient market acceptance, we could be prevented from or significantly delayed in achieving profitability and our business would be adversely affected.

39

Item 2.Unregistered Sales of Equity Securities, Use of Proceeds, and Issuer Purchases of Equity Securities

None.

Item 3.Defaults Upon Senior Securities

None.

Item 4.Mine Safety Disclosures

Not applicable.

Item 5.Other Information

Entry into a Material Definitive Agreement

On July 27, 2026, we and certain of our affiliates entered into Amendment No. 4 to Third Amended and Restated Loan and Security Agreement (the “Amendment”) with Hercules, which amended certain terms of the Third Amended and Restated Loan and Security Agreement, dated December 15, 2021 by and among us, certain of our subsidiaries, and Hercules, as amended by that certain Amendment No. 1 to Third Amended and Restated Loan and Security Agreement, dated as of May 12, 2023, Consent and Amendment No. 2 to Third Amended and Restated Loan and Security Agreement, dated as of June 28, 2024, and Amendment No. 3 to Third Amended and Restated Loan and Security Agreement.

The Amendment, among other things, extends the period we can draw the $100.0 million term loan tranche from June 15, 2027 to September 30, 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility otherwise remain unchanged.

The foregoing description of the Amendment does not purport to be complete and is qualified in its entirety by reference to the full text of the Amendment, a copy of which is filed as Exhibit 10.2 hereto and is incorporated herein by reference.

Adoption of 10b5-1 Trading Plans by Our Officers and Directors

During the three months ended June 30, 2026, the following adopted a “Rule 10b5-1 trading arrangement” (as defined in Item 408(a) of Regulation S-K) that is intended to satisfy the affirmative defense of Rule 10b5-1(c) under the Exchange Act and our policies on insider trading:

Name & Title

Date Adopted(1)

Aggregate Number of Ordinary Shares to be Purchased or Sold Pursuant to Trading Arrangement

Expiration Date(2)

David Meek, Non-executive Director

May 26, 2026

25,860

December 18, 2026

(1) Date of adoption of this Rule 10b5-1 trading arrangement is in accordance with applicable SEC rules and regulations. The first trade pursuant to this Rule 10b5-1 trading arrangement will be, in accordance with applicable SEC rules and regulations, on a date after the date of adoption of the Rule 10b5-1 trading arrangement, to the extent triggered under its terms.

(2) The Rule 10b5-1 trading arrangement is scheduled to expire on the date listed in the table, subject to earlier termination upon the sale of all shares subject to the Rule 10b5-1 trading arrangement, or as otherwise provided in the Rule 10b5-1 trading arrangement.

Other than those disclosed above, none of our directors or officers adopted, modified, or terminated a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” in each case as defined in Item 408 of Regulation S-K, during the three months ended June 30, 2026.

40

Item 6.Exhibits

See the Exhibit Index immediately preceding the signature page to this Quarterly Report on Form 10-Q for a list of exhibits filed or furnished with this report, which Exhibit Index is incorporated herein by reference.

41

EXHIBIT INDEX

3.1

Amended Articles of Association of uniQure N.V. (incorporated by reference to Exhibit 3.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on June 15, 2026).

10.1

Amended and Restated 2014 Share Incentive Plan of uniQure N.V. (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on June 15, 2026).

10.2*+

Amendment No. 4 to Third Amended and Restated Loan and Security Agreement, dated July 27, 2026, by and among uniQure biopharma, B.V., uniQure, Inc., uniQure IP B.V., uniQure N.V. and Hercules Capital, Inc.

31.1*

Certification of Chief Executive Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities and Exchange Act of 1934, as amended, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.

31.2*

Certification of Chief Financial Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities and Exchange Act of 1934, as amended, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.

32.1±

Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

101*

The following financial information from our Quarterly Report on Form 10-Q for the period ended June 30, 2026, filed with the Securities and Exchange Commission on July 29, 2026, is formatted in Inline Extensible Business Reporting Language (“iXBRL”): (i) Consolidated Balance Sheets; (ii) Consolidated Statements of Operations and Comprehensive Loss; (iii) Consolidated Statements of Shareholders’ Equity; (iv) Consolidated Statements of Cash Flows; and (v) Notes to Consolidated Financial Statements (tagged as blocks of text).

104*

The cover page from our Quarterly Report on Form 10-Q for the period ended June 30, 2026, filed with the Securities and Exchange Commission on July 29, 2026, is formatted in Inline Extensible Business Reporting Language (“iXBRL”).

*            Filed herewith.

±            Furnished herewith.

+Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.

42

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

UNIQURE N.V.

By: /s/ Matthew Kapusta

Matthew Kapusta

Chief Executive Officer

(Principal Executive Officer)

By: /s/ Christian Klemt

Christian Klemt

Chief Financial Officer

(Principal Financial and Accounting Officer)

Date: July 29, 2026

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ATTACHMENTS / EXHIBITS

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