UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

Merus N.V.

(Name of Issuer)

Common Shares, nominal value €0.09 per share

(Title of Class of Securities)

N5749R100

(CUSIP Number)

Thomas Dyrberg

Novo A/S

Tuborg Havnevej 19

Hellerup, Denmark DK-2900

+45 3527 6592

Copy to:

B. Shayne Kennedy, Esq.

Latham & Watkins LLP

650 Town Center Drive, 20^th Floor

Costa Mesa, CA 92626

Telephone: (714) 540-1235

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

May 19, 2016

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition which is subject of this Schedule 13D, and is filing this statement because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box.  ¨

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7(b) for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (the “Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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This Schedule 13D relates to the common shares, nominal value €0.09 per share (the “Common Shares”), of Merus N.V. (formerly Merus B.V.) (the “Issuer”), a corporation formed under the laws of the Netherlands. The Issuer’s principal office is located at Padualaan 8 (postvak 133), 3584 CH Utrecht, the Netherlands.

The name of each director and executive officer of both Novo A/S and the Foundation is set forth on Schedule I to this Schedule 13D.

The residence or business address of each director and executive officer of both Novo A/S and the Foundation is set forth on Schedule I to this Schedule 13D.

The Foundation is a Danish self-governing and profit-making foundation, whose objectives are to provide a stable basis for commercial and research activities undertaken by the group of Novo companies and to support scientific, humanitarian and social purposes through grants.

Prior to the Issuer’s initial public offering (the “IPO”), the Reporting Person held the following securities of the Issuer:

1,206,300 Class C preferred shares (the “Class C Shares”) acquired in a private placement on August 20, 2015 at a purchase price of EUR 6.66 per share for an aggregate purchase price of EUR 8,033,958. The holders of Class C Shares received a per share distribution at the rate of 8% of the original purchase price of such class per annum, compounding annually, and accruing on a daily basis, payable in kind upon the conversion of the Issuer’s preferred shares into Common Shares. As a result of a 1-for-1.80 reverse share split effected by the Issuer on May 6, 2016, Novo A/S held a total of 707,399 Class C Shares prior to the IPO (comprised of 670,167 Class C Shares and 37,232 Class C Shares issued in satisfaction of its entitlement to accrued distributions in kind). Upon the IPO closing, the Class C Shares automatically converted on a one-for-one basis for no additional consideration into 707,399 Common Shares.

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The purchase price of the Class C Shares was paid by Novo A/S from its working capital.

On May 19, 2016, the Reporting Person:

The acquisitions of Issuer securities made by Novo A/S, as described in this Schedule 13D, were for investment purposes. Novo A/S intends to review its investments in the Issuer on a continuing basis and any actions Novo A/S might undertake will be dependent upon its review of numerous factors from time to time, including, but not limited to: an ongoing evaluation of the Issuer’s business, financial condition, operations and prospects; price levels of the Issuer’s securities; general market, industry and economic conditions; the relative attractiveness of alternative business and investment opportunities; and other future developments. Novo A/S may, at any time and from time to time, acquire additional securities of the Issuer, or retain or sell all or a portion of the securities of the Issuer then held, in the open market or in privately negotiated transactions. Other than as described herein, Novo A/S currently does not have any plans or proposals that relate to, or would result in, any of the matters listed in Items 4(a)–(j) of Schedule 13D, although, depending on the factors discussed herein, Novo A/S may change its purpose or formulate different plans or proposals with respect thereto at any time. Jack B. Nielsen, a member of the supervisory board of the Issuer, is employed as a Senior Partner of Novo A/S. Mr. Nielsen is not deemed a beneficial owner of, and does not have a reportable pecuniary interest in, the Novo Shares (as defined below).

(a) Novo A/S beneficially owns 1,407,399 Common Shares (the “Novo Shares”), representing approximately 9.1% of the Issuer’s outstanding Common Shares, based upon 15,407,108 Common Shares outstanding as of the Issuer’s initial public offering as reported in the Issuer’s prospectus (Form 424B4) filed with the Securities and Exchange Commission on May 20, 2016.

(b) Novo A/S is a Danish limited liability company wholly owned by the Novo Nordisk Foundation. Novo A/S, through its Board of Directors (the “Novo Board”), has the sole power to vote and dispose of the Novo Shares. The Novo Board, currently comprised of Sten Scheibye, Goran Ando, Jeppe Christiansen, Steen Riisgaard and Per Wold-Olsen, may exercise voting and dispositive control over the Novo Shares only with the support of a majority of the Novo Board. As such, no individual member of the Novo Board is deemed to hold any beneficial ownership or reportable pecuniary interest in the Novo Shares. Jack B. Nielsen, a member of the supervisory board of the Issuer, is employed as a Senior Partner of Novo A/S. Mr. Nielsen is not deemed a beneficial owner of, and does not have a reportable pecuniary interest in, the Novo Shares. Except as described in this Schedule 13D, neither the Foundation nor any person listed on Schedule I has the power to direct the vote as to, or the disposition of the Novo Shares.

(c) Except as set forth in Item 3 of this Schedule 13D, Novo A/S has not effected any transactions in the Issuer’s Common Shares within the past 60 days and neither the Foundation nor any person listed on Schedule I has effected any transactions in the Issuer’s Common Shares within the past 60 days.

(d) Novo A/S does not know of any other person having the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of the Issuer’s Common Shares held in the name of the Novo A/S and reported herein.

(e) Not applicable.

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Registration Rights Agreement

Effective upon the closing date of the IPO, the Issuer, Novo A/S and certain other holders of the Issuer’s securities entered into a registration rights agreement, pursuant to which the Issuer granted demand registration rights, short-form registration rights and piggyback registration rights to such shareholders. The rights of any shareholder under such agreement will terminate upon the earlier to occur of: (a) the fourth anniversary of the Issuer’s IPO, and (b) such time as Rule 144 or another similar exemption under the Securities Act of 1933, as amended, is available for the sale of all such shareholder’s Common Shares without limitation during a three-month period without registration.

Lock-Up Agreement

Novo A/S entered into a letter agreement with the Issuer and the Underwriters, on September 4, 2015 which was subsequently amended on April 6, 2016 (the “Lock-Up Agreement”). Pursuant to such agreement Novo A/S agrees, without the prior written consent of the Underwriters and subject to limited exceptions, not to offer, pledge, announce the intention to sell, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase or otherwise dispose of, directly or indirectly, or enter into any swap or other agreement that transfers, in whole or in part, any of the economic consequences of ownership of the Common Shares or such other securities for a period of 180 days after the date of the final prospectus used to sell Common Shares in the IPO. The Lock-Up Agreement automatically terminates and shall be of no further force or effect following the expiration of the Lock-Up Period.

The descriptions contained in this Statement on Schedule 13D of the Registration Rights Agreement and the Lock-Up Agreement are summaries only and are qualified in their entireties by the actual terms of each such agreement, which are incorporated herein by this reference. See Item 7 “Material to be Filed as Exhibits.”

Except for the Registration Rights Agreement and the Lock-Up Agreement, neither Novo A/S, the Foundation, nor any person named in Schedule I has entered into any contracts, arrangements, understandings or relationships with respect to securities of the Issuer.

Exhibit A: Form of Registration Rights Agreement (incorporated by reference to Exhibit 4.1 of Form F-1 Registration Statement of the Issuer filed January 21, 2016 (File No. 333-2074990)).

Exhibit B: Form of Lock-Up Agreement, as amended.

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SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Schedule I

Information regarding each director and executive officer of both Novo A/S and the Novo Nordisk Foundation is set forth below.