As filed with the Securities and Exchange Commission on July 29, 2026

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Registration No. 333-

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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

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FORM S-8

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REGISTRATION STATEMENT UNDER

THE SECURITIES ACT OF 1933

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UNIQURE N.V.

(Exact Name of Registrant as Specified in its Charter)

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uniQure N.V. Amended and Restated 2014 Share Incentive Plan

(Full Title of the Plan)

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Matthew Kapusta

Chief Executive Officer

1 Hartwell Place

Lexington, MA 02421

(Name and Address of Agent For Service)

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Tel: +1 339 970 7000

(Telephone Number, Including Area Code, of Agent For Service)

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Copies to:

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Jeannette Potts

Chief Legal Officer

1 Hartwell Place

Lexington, MA 02421

+1 339 970 7000

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Timothy J. Corbett

Morgan, Lewis & Bockius LLP

One Federal Street

Boston, MA 02110

+1 617 341 7700

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

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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 7(a)(2)(B) of the Securities Act. ☐

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EXPLANATORY NOTE

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This Registration Statement on Form S-8 (this “Registration Statement”) is being filed by uniQure N.V. (the “Registrant”) solely for the purpose of registering an additional 350,000 ordinary shares, par value €0.05 per share, of the Registrant (the “Ordinary Shares”) to be offered to participants under the Registrant’s Amended and Restated 2014 Share Incentive Plan, which was originally adopted at the annual general meeting of the Registrant’s shareholders on January 9, 2014 and was subsequently amended or amended and restated, as applicable, as of June 10, 2015, June 15, 2016, June 13, 2018, June 16, 2021, November 15, 2023, June 18, 2024, June 11, 2025, and June 10, 2026 (as so amended or as amended and restated to date, the “2014 Plan”).

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On April 14, 2026, an amendment to the 2014 Plan (in the form then in effect) was approved by the board of directors of the Registrant and was subsequently approved by the Registrant’s shareholders at its annual general meeting on June 10, 2026 to increase the number of Ordinary Shares reserved for issuance under the 2014 Plan by an additional 350,000 shares.

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The Ordinary Shares registered hereby are in addition to and of the same class as those on the Registrant’s registration statements on Form S-8 registering (i) 1,531,471 Ordinary Shares issuable under the 2014 Plan previously filed with the Securities and Exchange Commission (the “Commission”) on August 6, 2014 (File No. 333-197887), (ii) 4,070,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on May 15, 2017 (File No. 333-218005), (iii) 3,000,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on June 14, 2018 (File No. 333-225629), (iv) 4,000,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on July 20, 2021 (File No. 333-258036), (v) 1,750,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on February 28, 2024 (File No. 333-277439), (vi) 1,500,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on August 1, 2024 (File No. 333-281165), and (vii) 2,400,000 Ordinary Shares issuable under the 2014 Plan previously filed with the Commission on June 30, 2025 (File No. 333-288413) (collectively, the “Previous Registration Statements”). In accordance with General Instruction E to Form S-8, the contents of the Previous Registration Statements and the contents incorporated by reference therein are hereby incorporated herein by reference and the information required by Part II is omitted, except as supplemented by the information set forth below.

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PART II

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INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

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Item 3. Incorporation of Documents by Reference.

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The following documents are incorporated herein by reference:

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(a) The Registrant’s Annual Report on Form 10-K for fiscal year ended December 31, 2025 filed with the Commission on March 2, 2026;

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(b) The Registrant’s Quarterly Reports on Form 10-Q filed with the Commission on May 5, 2026 and July 29, 2026;

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(c) The information specifically incorporated by reference into the Registrant’s Annual Report on Form 10-K for the year ended December 31, 2025 from the Registrant's Definitive Proxy Statement on Schedule 14A, filed with the Commission on April 27, 2026; and

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(d) The description of the securities contained in the Registrant’s registration statement on Form 8-A (Registration No. 001-36294) filed with the Commission on January 31, 2014, under the Securities Exchange Act of 1934, as amended (the “Exchange

Act”), including any amendment or report filed for the purpose of updating such description.

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All documents filed by the Registrant pursuant to Section 13(a), 13(c), 14 or 15(d) of the Exchange Act subsequent to the filing of this Registration Statement and prior to the filing of a post-effective amendment which indicates that all securities offered hereby have been sold or which deregisters all securities then remaining unsold, shall be deemed to be incorporated by reference into this Registration Statement and to be a part hereof from the date of filing such documents, except as to specific sections of such documents as set forth therein. Any statement contained in a document incorporated or deemed to be incorporated by reference herein shall be deemed to be modified or superseded for purposes of this Registration Statement to the extent that a statement contained in any subsequently filed document which also is deemed to be incorporated by reference herein modifies or supersedes such statement.

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Item 8. Exhibits.

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A list of exhibits filed herewith is contained in the Exhibit Index that immediately precedes the signature page hereto and is incorporated herein by reference.

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EXHIBIT INDEX

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* Filed herewith.

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SIGNATURES

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Pursuant to the requirements of the Securities Act of 1933, the registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8 and has duly caused this registration statement to be signed on its behalf by the undersigned, thereunto duly authorized, in Amsterdam, the Netherlands, on July 29, 2026.

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POWER OF ATTORNEY AND SIGNATURES

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KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Matthew Kapusta and Christian Klemt, and each of them, as his or her true and lawful agent, proxy and attorney-in-fact, each acting alone, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to (i) act on, sign, and file with the SEC any and all amendments (including post-effective amendments) to this registration statement together with all schedules and exhibits thereto, (ii) act on, sign and file such certificates, instruments, agreements and other documents as may be necessary or appropriate in connection therewith, (iii) act on and file any supplement to any prospectus included in this registration statement or any such amendment or any subsequent registration statement filed pursuant to Rule 462(b) under the Securities Act and (iv) take any and all actions which may be necessary or appropriate to be done, as fully for all intents and purposes as he or she might or could do in person, hereby approving, ratifying and confirming all that such agent, proxy and attorney-in-fact or any of his substitutes may lawfully do or cause to be done by virtue thereof.

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Pursuant to the requirements of the Securities Act, as amended, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated.

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AUTHORIZED UNITED STATES REPRESENTATIVE

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Pursuant to the requirement of the Securities Act of 1933, the undersigned, the duly authorized representative in the United States of the aforementioned Registrant, has signed this Registration Statement on July 29, 2026.

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Exhibit 5.1

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To the Company:

We have acted as legal counsel as to Dutch law to the Company in connection with the Plan and the filing of the Registration Statement with the SEC. This opinion letter is rendered to you in order to be filed with the SEC as an exhibit to the Registration Statement.

Capitalised terms used in this opinion letter have the meanings set forth in Exhibit A to this opinion letter. The headings used in this opinion letter are for convenience of reference only and are not to affect its construction or to be taken into consideration in its interpretation.

This opinion letter is strictly limited to the matters stated in it and may not be read as extending by implication to any matters not specifically referred to in it. Nothing in this opinion letter should be taken as expressing an opinion in respect of any representations or warranties, or other information, contained in any document reviewed by us in connection with this opinion letter.

In rendering the opinions expressed in this opinion letter, we have reviewed and relied upon a pdf copy of the Plan, a draft of the Registration Statement and pdf copies of the Corporate Documents and we have assumed that Awards under the Plan shall be made for bona fide commercial reasons. We have not investigated or verified any factual matter disclosed to us in the course of our review.

This opinion letter sets out our opinion on certain matters of the laws with general applicability of the Netherlands, and, insofar as they are directly applicable in the Netherlands, of the European Union, as at today's date and as presently interpreted under published authoritative case law of the Dutch courts, the General Court and the Court of Justice of the European Union. We do not express any opinion on Dutch or European competition law, data protection law, tax law, securitisation law or regulatory law. No undertaking is assumed on our part to revise, update or amend this opinion letter in connection with, or to notify or inform you of, any developments and/or changes of Dutch law subsequent to today's date. We do not purport to opine on the consequences of amendments to the Plan, the Registration Statement or the Corporate Documents subsequent to the date of this opinion letter.

The opinions expressed in this opinion letter are to be construed and interpreted in accordance with Dutch law. The competent courts at Amsterdam, the Netherlands, have exclusive jurisdiction to settle any issues of interpretation or liability arising out of or in connection with this opinion letter. Any legal relationship arising out of or in connection with this opinion letter (whether contractual or non-

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contractual), including the above submission to jurisdiction, is governed by Dutch law and shall be subject to the general terms and conditions of NautaDutilh. Any liability arising out of or in connection with this opinion letter shall be limited to the amount which is paid out under NautaDutilh's insurance policy in the matter concerned. No person other than NautaDutilh may be held liable in connection with this opinion letter.

In this opinion letter, legal concepts are expressed in English terms. The Dutch legal concepts concerned may not be identical in meaning to the concepts described by the English terms as they exist under the law of other jurisdictions. In the event of a conflict or inconsistency, the relevant expression shall be deemed to refer only to the Dutch legal concepts described by the English terms.

For the purposes of this opinion letter, we have assumed that:

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(ontbonden), (ii) ceased to exist pursuant to a merger (fusie) or a division (splitsing), (iii) been converted (omgezet) into another legal form, either national or foreign (except pursuant to the Deed of Conversion), (iv) had its assets placed under administration (onder bewind gesteld), (v) been declared bankrupt (failliet verklaard), (vi) been granted a suspension of payments (surseance van betaling verleend), (vii) started or become subject to statutory proceedings for the restructuring of its debts (akkoordprocedure) or (viii) been made subject to similar proceedings in any jurisdiction or otherwise been limited in its power to dispose of its assets;

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4

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Based upon and subject to the foregoing and subject to the qualifications set forth in this opinion letter and to any matters, documents or events not disclosed to us, we express the following opinions:

Incorporation and Corporate Status

Plan Shares

The opinions expressed above are subject to the following qualifications:

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circumstances that must be taken into account, in particular whether the interests of the Company are served by making Awards under the Plan since this is a matter of fact.

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6

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We consent to the filing of this opinion letter as an exhibit to the Registration Statement. In giving this consent, we do not admit or imply that we are a person whose consent is required under Section 7 of the United States Securities Act of 1933, as amended, or any rules and regulations promulgated thereunder.

Sincerely yours,

/s/ NautaDutilh N.V.

NautaDutilh N.V.

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EXHIBIT A

LIST OF DEFINITIONS

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9

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Exhibit 23.2

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Consent of Independent Registered Public Accounting Firm

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We consent to the use of our report dated March 2, 2026, with respect to the consolidated financial statements of uniQure N.V., and the effectiveness of internal control over financial reporting, incorporated herein by reference.

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/s/ KPMG Accountants N.V.

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Amstelveen, The Netherlands

July 29, 2026