UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 1)*

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 amendment (“Amendment No. 1”), amends the Schedule 13D originally filed with the Securities and Exchange Commission (the “Commission”) on May 26, 2016 (the “Initial Schedule”). Except as specifically amended by this Amendment No. 1, each Item of the Initial Schedule remains unchanged. All capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Initial Schedule.

This Amendment No. 1 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.

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). Immediately prior to the IPO closing, (i) the Class C Shares automatically converted on a one-for-one basis for no additional consideration into 707,399 Common Shares (the “Converted Shares”) and (ii) the Reporting Person received 3,018 additional Common Shares in satisfaction of its entitlement to accrued distributions in kind (the “Accrued Shares”).

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:

(a) Novo A/S beneficially owns 1,410,417 Common Shares (the “Novo Shares”), representing approximately 8.8% of the Issuer’s outstanding Common Shares, based upon 16,080,356 Common Shares outstanding as reported by the Issuer.

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(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 Amendment No. 1, 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 Amendment No. 1, 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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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.