Exhibit 5.1

Rutgers Posch Visée Endedijk N.V.

Herengracht 466, 1017 CA Amsterdam

P.O. Box 10896, 1001 EW Amsterdam

The Netherlands

T + 31(0)20 891 3900 | F + 31(0)20 891 3901

www.rutgersposch.com

Draft

uniQure B.V. (the “Issuer”)

Meibergdreef 61

1105 BA Amsterdam

The Netherlands

Date:   [  ] 2013

uniQure B.V. - SEC Exhibit 5 opinion letter

Dear Sirs,

1.Introduction

We have acted as Dutch legal counsel to the Issuer in connection with the Registration (as defined below).

2.Definitions

Certain terms used in this opinion are defined in Annex 1 (Definitions) hereto.

3.Dutch Law

We express no opinion or statement on any law other than Dutch Law. Our investigation has further been limited to the text of documents. We have not investigated the meaning and effect of any document governed by a law other than Dutch Law. The opinions and statements expressed herein are rendered only as of the date of this opinion and we assume no obligation to advise you of facts, circumstances, events or changes in Dutch Law that may hereafter arise or be brought to our attention and that may alter, affect or modify the opinions or statements expressed herein.

4.Scope of investigation; definitions

For purposes of this opinion, we have examined and relied solely upon the following documents:

Rutgers & Posch is the tradename of Rutgers Posch Visée Endedijk N.V. in Amsterdam (Traderegister no. 56919891). The general terms and conditions of Rutgers & Posch, which stipulate a limitation of liability, the applicability of Dutch law and the exclusive jurisdiction of the district court in Amsterdam, are applicable to all work performed. The general terms and conditions are available at www.rutgersposch.com.

4.1a copy of the Registration Statement;

4.2a copy of the Deed of Incorporation;

4.3a copy of the Extract;

4.4a copy of the Shareholders Register;

4.5a copy of the IPO Resolution;

4.6[a copy/the form] of the Shareholders Resolution;

4.7a copy of the Board Certificate;

4.8the form of the Deed of Conversion containing the Issuer’s articles of association (statuten) as will be in force at the time of the Issue of the Registration Shares;

4.9the form of the Underwriting Agreement;

4.10[the form of each Pricing Resolution]; and

4.11the form of  the Deed of Issuance.

In addition, we have examined such documents, and performed such other investigations, as we considered necessary for the purpose of this opinion.

5.Assumptions

For the purpose of this opinion, we have assumed that:

5.1all copies of documents conform to the originals and that all originals are authentic and complete;

5.2each signature is the genuine signature of the individual concerned;

5.3all factual matters, statements in documents, confirmations and other results of our investigation, relied upon or assumed herein, were true and accurate on the date of signing of the Documents and remain true and accurate on the date hereof;

5.4The Registration Statement has been or will have been filed with the SEC in the form referred to in this opinion;

5.5The Deed of Conversion and Pricing Resolution will have been executed in the form

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referred to in this opinion; and

5.6The Registration Shares will have been validly accepted by the subscriber for them.

6.Opinions

Based upon the foregoing and subject to any factual matters and documents not disclosed to us in the course of our investigation, and subject to the qualifications and limitations stated hereafter, we express the following opinion:

6.1The Registration Shares, when issued, fully paid for and delivered in accordance with the terms of the Deed of Issuance will be validly issued, fully paid and non-assessable(1).

7.Reliance

7.1This opinion is furnished to you in order to be filed as an exhibit to the Registration Statement and may be relied upon for the purpose of the Registration. We consent to the filing of this opinion as Exhibit 5 to the Registration Statement and further consent to the reference to our firm in the Registration Statement under the caption “Legal Matters”. In giving such consent, we do not admit that we come within the category of persons whose consent is required under section 7 of the U.S. Securities Act of 1933 or the rules and regulations promulgated thereunder.

7.2This opinion  may only relied upon under the express condition that it and any issues of interpretation or liability arising thereunder will be governed by Dutch Law and be brought before a court of the Netherlands. In addition, this opinion may only be relied upon under the express condition and limitation that any possible liability of Rutgers Posch Visée Endedijk N.V., its shareholders (including its directors) and employees is limited to the amount available and payable under Rutgers Posch Visée Endedijk N.V.’s professional malpractice insurance coverage.

Yours faithfully,

Rutgers Posch Visée Endedijk N.V.

(1)  The term “non-assessable” has no equivalent in Dutch and as used in this opinion it means that a holder of a share will not by reason of merely being such a holder, be subject to assessment or calls by the Issuer or its creditors for further payment (in addition to the amount required for the share to be fully paid) on such share.

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Annex 1

Definitions

“Board Certificate”  means the certificate dated the date of this opinion attached as Annex 2 hereto;

“Chamber of Commerce” means the Chamber of Commerce (Kamer van Koophandel en Fabrieken) of Amsterdam;

“Deed of Conversion” means the draft deed of conversion and amendment of the articles of association dated [ ] 2013 providing for the conversion of the Issuer from a private company with limited liability (besloten vennootschap met beperkte aansprakelijkheid) into a public limited liability company (naamloze vennootschap) and amendment of its articles of association;

“Deed of Issuance” means a copy of the [draft] private deed of issuance (onderhandse akte van uitgifte) in respect of the Registration Shares dated [ ] 2013;

“Deed of Incorporation” means the Company’s deed of incorporation dated 9 January 2013 as deposited with the Chamber of Commerce;

“Dutch Law” means the laws of the Kingdom of the Netherlands excluding Aruba, Bonaire, Curaçao, Saba, Sint Eustatius and Sint Maarten (“the Netherlands”) as they currently stand and are applied by the courts of the Netherlands but excluding unpublished case law and case law available in electronic form only;

“Extract” means the  copy of a trade register extract regarding the Company obtained from the Chamber of Commerce and dated  [ ] 2013;

“IPO Resolution” means the resolutions of the Issuer’s supervisory board set out in the [written resolutions dated /minutes of its meeting held on] [ ] 2013, including a resolution to appoint a pricing committee (the “Pricing Committee”) and delegate to the Pricing Committee the authority to (i) determine the number of and issue price for the Registration Shares, subject to certain conditions, and (ii) approve the terms (including discounts and commissions) of an underwriting agreement;

“Insolvency Proceedings” means each of the proceedings listed In Annex A or B of Council Regulation (EC) No 1346/2000 of 29 May 2000 on insolvency proceedings (OJ 2000, L 160, 1), as amended;

“Issue Authorisation Maximum” is defined in the definition of “Shareholders

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Resolution”;

“Pricing Resolution” means:

(a)a draft written resolution of the Issuer’s management board dated [ ] 2013, including resolutions to:

(i)propose the number of and issue price for the Registration Shares;

(ii)propose to grant an option for a number of Registration Shares to be issued in addition to the number of Registration Shares referred to in (i);

(iii)propose to issue the Registration Shares; and

(iv)propose to exclude all pre-emption rights (voorkeursrechten) in respect of the issue of Registration Shares and the grant of the option to acquire Registration Shares;

(b)a draft written resolution of the Pricing Committee dated [ ] 2013 to approve the resolution of the management board referred to in (a);

(c)a draft written resolution of the Issuer’s [management board] dated [ ] 2013, to adopt the resolutions referred to in (a).

(d)a draft written resolution of the Issuer’s supervisory board dated [ ] 2013 to approve the resolution of the management board referred to in (a); and

(e)a draft written resolution of the Issuer’s management board dated [ ] 2013 to (i) determine the number of Registration Shares to be issued in addition to the number of Registration Shares referred to in paragraph (a)(ii) and (ii) issue such Registration Shares;

“Registration” means the registration of the Registration Shares with the SEC under the U.S. Securities Act;

“Registration Shares” means a maximum of [ ] ordinary shares, nominal value EUR [0.05] each, in the Issuer’s share capital, to be issued by the Issuer pursuant to the IPO Resolution, the Shareholders Resolution and the Pricing Resolution;

“Registration Statement” means the registration statement on form F-1 (Registration No. 333-188855) in relation to the Registration to be filed with the SEC on the date hereof (excluding any documents incorporated by reference in it and any exhibits to

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it);

“SEC” means the U.S. Securities and Exchange Commission;

“Shareholders Register” means the Issuer’s shareholders register;

“Shareholders Resolution” means the [written] resolutions of the Issuer’s general meeting of shareholders [set out in the extract from the minutes of its meeting held on / dated] [ ] 2013, including a resolution to designate the Issuer’s management board as the corporate body authorised to resolve, subject to the approval of the Issuer’s supervisory board, to issue ordinary shares in the Issuer’s capital up to a maximum of [ ] (the “Issue Authorisation Maximum”) and to exclude all pre-emption rights in respect thereof;

“Underwriting Agreement” means the draft underwriting agreement entered into between the Underwriters as representatives for the several underwriters named in Schedule A of the underwriting agreement dated [ ] 2013; and

“U.S. Securities Act” means the U.S. Securities Act of 1933, as amended.

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Annex 2

Board Certificate

From:  the management board of uniQure B.V.

Dated: [ ] 2013

The undersigned:

1.Jörn Aldag; and

2.Piers Morgan,

acting in their capacity as managing directors of uniQure B.V., a private limited liability company (besloten vennootschap met beperkte aansprakelijkheid) incorporated under Dutch law, having its corporate seat in Amsterdam, the Netherlands and registered with the Dutch trade register of the Chamber of Commerce under number 54385229 (the “Issuer”),

Background:

  I.The Issuer intends to seek the Registration with the SEC of the Registration Shares;

 II.In connection with the Registration, on the date of this Board Certificate, Rutgers Posch Visée Endedijk N.V. intends to issue a legal opinion in the form attached to this certificate (the “Legal Opinion”);

III.This Board Certificate is the “Board Certificate” as defined in the Legal Opinion; and

IV.The undersigned make the certifications in this Board Certificate after due and careful consideration and after having made all necessary enquiries.

1.Construction

2.1Terms defined in the Legal Opinion have the same meaning in this Board Certificate; and

2.2In this Board Certificate “including” means “including without limitation”.

2.Certification

Each undersigned certifies the following:

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2.1Authenticity

As at the date of this Board Certificate:

i)all information regarding the Issuer registered or on file with the Dutch Trade Register of the Chamber of Commerce; and

ii)all information in the Shareholders Register,

is correct, complete and up to date.

2.2Solvency

The Issuer is not the subject of any Insolvency Proceedings, emergency measure (noodregeling), a non-insolvency dissolution, or a statutory merger or demerger.

2.3Issue

The maximum number of Registration Shares to be issued will not exceed the Issue Authorisation Maximum.

2.4General

No undersigned is aware of:

i)any claim (whether actual or threatened and including any claim, litigation, arbitration or administrative or regulatory proceedings) to the contrary of the certifications in this Board Certificate; or

ii)any fact or circumstance which he or she understands or suspects has or might have any impact on the correctness of the Legal Opinion and which has not been disclosed to Rutgers Posch Visée Endedijk N.V. in writing.

3.Reliance

Rutgers Posch Visée Endedijk N.V. may rely on this Board Certificate (without personal liability for the undersigned).

In evidence whereof this Board Certificate was signed in the manner set out below.

Name: Jörn Aldag

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Name: Piers Morgan

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