Document:

EX-10.4

 Exhibit 10.4 

MERUS N.V. 

INDEMNIFICATION AGREEMENT 

THIS INDEMNIFICATION AGREEMENT (the “Agreement”) is made and entered into as of
            , 20[16] between Merus N.V., a public company with limited liability incorporated under the laws of the Netherlands (the “Company”), and [Name]
(“Indemnitee”). 
 WITNESSETH THAT: 

WHEREAS, highly competent persons have become more reluctant to serve corporations as supervisory board members, management board members or
in other capacities unless they are provided with adequate protection through insurance or adequate indemnification against inordinate risks of claims and actions against them arising out of their service to and activities on behalf of the
corporation; 
 WHEREAS, the Management Board of the Company (the “Management Board”) has determined that, in order
to attract and retain qualified individuals, the Company will attempt to maintain on an ongoing basis, at its sole expense, liability insurance to protect persons serving the Company and its subsidiaries from certain liabilities. Although the
furnishing of such insurance has been a customary and widespread practice among United States-based corporations and other business enterprises, the Company believes that, given current market conditions and trends, such insurance may be available
to it in the future only at higher premiums and with more exclusions. At the same time, the supervisory board of the Company (the “Supervisory Board”) members, Management Board members, and other persons in service to
corporations or business enterprises are being increasingly subjected to expensive and time-consuming litigation relating to, among other things, matters that traditionally would have been brought only against the Company or business enterprise
itself. The Articles of Association of the Company require indemnification of the Supervisory Board members and its Management Board members of the Company. The Articles of Association expressly provide that the indemnification provisions set forth
therein are not exclusive, and thereby contemplate that contracts may be entered into between the Company and members of the Supervisory Board, Management Board members and other persons with respect to indemnification; 

WHEREAS, the uncertainties relating to such insurance and to indemnification have increased the difficulty of attracting and retaining such
persons; whereby it is to the best interests of the Company’s shareholders and that the Company should act to assure such persons that there will be increased certainty of such protection in the future; 

WHEREAS, it is reasonable, prudent and necessary for the Company contractually to obligate itself to indemnify, and to advance expenses on
behalf of, such persons to the fullest extent permitted by applicable law so that they will serve or continue to serve the Company free from undue concern that they will not be so indemnified; 

WHEREAS, this Agreement is a supplement to and in furtherance of the Articles of Association of the Company and any resolutions adopted
pursuant thereto, and shall not be deemed a substitute therefor, nor to diminish or abrogate any rights of Indemnitee thereunder; [and] 

 NOW, THEREFORE, in consideration of Indemnitee’s agreement to serve as an [Management Board
member] [Supervisory Board member] from and after the date hereof, the parties hereto agree as follows: 
 1. Indemnity of
Indemnitee. The Company hereby agrees to hold harmless and indemnify Indemnitee to the fullest extent permitted by law, as such may be amended from time to time. In furtherance of the foregoing indemnification, and without limiting the
generality thereof: 
 (a) Proceedings Other Than Proceedings by or in the Right of the Company. Indemnitee shall be entitled
to the rights of indemnification provided in this Section l(a) if, by reason of his Corporate Status (as hereinafter defined), the Indemnitee is, or is threatened to be made, a party to or participant in any Proceeding (as hereinafter
defined) other than a Proceeding by or on behalf of the Company. Pursuant to this Section 1(a), Indemnitee shall be indemnified against all Expenses (as hereinafter defined), judgments, penalties, fines and amounts paid in settlement
actually and reasonably incurred by him, or on his behalf, in connection with such Proceeding or any claim, issue or matter therein to the extent this directly relates to this position as member of the [Management Board / Supervisory Board] in each
case to the fullest extent permitted by applicable law, if the Indemnitee acted in good faith and in a manner the Indemnitee reasonably believed to be in or not opposed to the best interests of the Company, and with respect to any criminal
Proceeding, had no reasonable cause to believe the Indemnitee’s conduct was unlawful. 
 (b) Proceedings by or in the Right of the
Company. Indemnitee shall be entitled to the rights of indemnification provided in this Section 1(b) if, by reason of his Corporate Status, the Indemnitee is, or is threatened to be made, a party to or participant in any Proceeding
brought by or in the right of the Company. Pursuant to this Section 1(b), Indemnitee shall be indemnified against all Expenses actually and reasonably incurred by the Indemnitee, or on the Indemnitee’s behalf in connection with such
Proceeding if the Indemnitee acted in good faith and in a manner the Indemnitee reasonably believed to be in or not opposed to the best interests of the Company; provided, however, if applicable law so provides, no indemnification against such
Expenses shall be made in respect of any claim, issue or matter in such Proceeding as to which Indemnitee shall have been adjudged to be liable to the Company. 

(c) Indemnification for Expenses of a Party Who is Wholly or Partly Successful. Notwithstanding any other provision of this
Agreement, to the extent that Indemnitee is, by reason of his Corporate Status, a party to and is successful, on the merits or otherwise, in any Proceeding, he shall be indemnified to the maximum extent permitted by law, as such may be amended from
time to time, against all Expenses actually and reasonably incurred by him or on his behalf in connection therewith. If Indemnitee is not wholly successful in such Proceeding but is successful, on the merits or otherwise, as to one or more but
less than all claims, issues or matters in such Proceeding, the Company shall indemnify Indemnitee against all Expenses actually and reasonably incurred by him or on his behalf in connection with each successfully resolved claim, issue or
matter. For purposes of this Section and without limitation, the termination of any claim, issue or matter in such a Proceeding by dismissal, with or without prejudice, shall be deemed to be a successful result as to such claim, issue or
matter. 
 2. Additional Indemnity. In addition to, and without regard to any limitations on, the indemnification provided for
in Section 1 of this Agreement, the Company 

 
shall and hereby does indemnify and hold harmless Indemnitee against all Expenses, judgments, penalties, fines and amounts paid in settlement actually and reasonably incurred by him or on his
behalf if, by reason of his Corporate Status, he is, or is threatened to be made, a party to or participant in any Proceeding (including a Proceeding by or in the right of the Company), including, without limitation, all liability arising out of the
negligence or active or passive wrongdoing of Indemnitee. The only limitation that shall exist upon the Company’s obligations pursuant to this Agreement shall be that the Company shall not be obligated to make any payment to Indemnitee that is
finally determined (under the procedures, and subject to the presumptions, set forth in Sections 6 and 7 hereof) to be (i) intentional, (ii) grossly negligent, or (iii) unlawful. 

3. Contribution. 
 (a)
Whether or not the indemnification provided in Sections 1 and 2 hereof is available, in respect of any threatened, pending or completed action, suit or proceeding in which the Company is jointly liable with Indemnitee (or would be if
joined in such action, suit or proceeding), the Company shall pay, in the first instance, the entire amount of any judgment or settlement of such action, suit or proceeding without requiring Indemnitee to contribute to such payment and the Company
hereby waives and relinquishes any right of contribution it may have against Indemnitee. The Company shall not enter into any settlement of any action, suit or proceeding in which the Company is jointly liable with Indemnitee (or would be if
joined in such action, suit or proceeding) unless such settlement provides for a full and final release of all claims asserted against Indemnitee. 

(b) Without diminishing or impairing the obligations of the Company set forth in the preceding subparagraph, if, for any reason, Indemnitee
shall elect or be required to pay all or any portion of any judgment or settlement in any threatened, pending or completed action, suit or proceeding in which the Company is jointly liable with Indemnitee (or would be if joined in such action, suit
or proceeding), the Company shall contribute to the amount of Expenses, judgments, fines and amounts paid in settlement actually and reasonably incurred and paid or payable by Indemnitee in proportion to the relative benefits received by the Company
and all Management Board members, Supervisory Board members or employees of the Company, other than Indemnitee, who are jointly liable with Indemnitee (or would be if joined in such action, suit or proceeding), on the one hand, and Indemnitee, on
the other hand, from the transaction or events from which such action, suit or proceeding arose; provided, however, that the proportion determined on the basis of relative benefit may, to the extent necessary to conform to law, be further adjusted
by reference to the relative fault of the Company and all Management Board members, Supervisory Board members or employees of the Company other than Indemnitee who are jointly liable with Indemnitee (or would be if joined in such action, suit or
proceeding), on the one hand, and Indemnitee, on the other hand, in connection with the transaction or events that resulted in such expenses, judgments, fines or settlement amounts, as well as any other equitable considerations which applicable law
may require to be considered. The relative fault of the Company and all Management Board members, Supervisory Board members or employees of the Company, other than Indemnitee, who are jointly liable with Indemnitee (or would be if joined in
such action, suit or proceeding), on the one hand, and Indemnitee, on the other hand, shall be determined by reference to, among other things, the degree to which their actions were motivated by intent to gain personal profit or advantage, the
degree to which their liability is primary or secondary and the degree to which their conduct is active or passive. 

 (c) The Company hereby agrees to fully indemnify and hold Indemnitee harmless from any claims of
contribution which may be brought by Management Board members, Supervisory Board members or employees of the Company, other than Indemnitee, who may be jointly liable with Indemnitee. 

(d) To the fullest extent permissible under applicable law, if the indemnification provided for in this Agreement is unavailable to
Indemnitee for any reason whatsoever, the Company, in lieu of indemnifying Indemnitee, shall contribute to the amount incurred by Indemnitee, whether for judgments, fines, penalties, excise taxes, amounts paid or to be paid in settlement and/or for
Expenses, in connection with any claim relating to an indemnifiable event under this Agreement, in such proportion as is deemed fair and reasonable in light of all of the circumstances of such Proceeding to be determined pursuant to Section 5
in order to reflect (i) the relative benefits received by the Company and Indemnitee as a result of the event(s) and/or transaction(s) giving cause to such Proceeding and/or (ii) the relative fault of the Company (and its Supervisory Board members,
Management Board members, employees and agents) and Indemnitee in connection with such event(s) and/or transaction(s). 
 3.
Indemnification for Expenses of a Witness. Notwithstanding any other provision of this Agreement, to the extent that Indemnitee is, by reason of his Corporate Status, a witness, or is made (or asked) to respond to discovery requests, in
any Proceeding to which Indemnitee is not a party, he shall be indemnified against all Expenses actually and reasonably incurred by him or on his behalf in connection therewith. 

4. Advancement of Expenses. Notwithstanding any other provision of this Agreement, the Company shall advance all Expenses incurred
by or on behalf of Indemnitee in connection with any Proceeding by reason of Indemnitee’s Corporate Status within thirty (30) days after the receipt by the Company of a statement or statements from Indemnitee requesting such advance or advances
from time to time, whether prior to or after final disposition of such Proceeding. Such statement or statements shall reasonably evidence the Expenses incurred by Indemnitee and shall include or be preceded or accompanied by a written
undertaking by or on behalf of Indemnitee to repay any Expenses advanced if it shall ultimately be determined that Indemnitee is not entitled to be indemnified against such Expenses. Any advances and undertakings to repay pursuant to this
Section 4 shall be unsecured and interest free. 
 5. Procedures and Presumptions for Determination of Entitlement to
Indemnification. It is the intent of this Agreement to secure for Indemnitee rights of indemnity that are as favorable as may be permitted under applicable law. Accordingly, the parties agree that the following procedures and
presumptions shall apply in the event of any question as to whether Indemnitee is entitled to indemnification under this Agreement: 
 (a)
To obtain indemnification under this Agreement, Indemnitee shall submit to the Company a written request, including therein or therewith such documentation and information as is reasonably available to Indemnitee and is reasonably necessary to
determine whether and to what extent Indemnitee is entitled to indemnification. The [Head of Legal] of the Company shall, promptly upon receipt of such a request for indemnification, advise the Management Board and Supervisory Board in writing
that Indemnitee has requested indemnification. Notwithstanding the foregoing, any failure of Indemnitee to provide such a request to the Company, or to provide such a request in a timely fashion, shall not relieve the Company of any liability
that it may have to Indemnitee unless, and to the extent that, such failure actually and materially prejudices the interests of the Company. 

 (b) Upon written request by Indemnitee for indemnification pursuant to the first sentence of
Section 5(a) hereof, a determination with respect to Indemnitee’s entitlement thereto shall be made in the specific case by one of the following four methods, which shall be at the election of the Supervisory Board: (1) by a
majority vote of the disinterested Supervisory Board members, even though less than a quorum, (2) by a committee of disinterested Supervisory Board members designated by a majority vote of the disinterested Supervisory Board members, even though
less than a quorum, (3) if there are no disinterested Supervisory Board members or if the disinterested Supervisory Board members so direct, by independent legal counsel in a written opinion to the Supervisory Board, a copy of which shall be
delivered to the (i) Management Board, and (ii) Indemnitee, or (4) if so directed by the Supervisory Board, by the shareholders of the Company. For purposes hereof, disinterested Supervisory Board members are those members of the Supervisory
Board who are not parties to the action, suit or proceeding in respect of which indemnification is sought by Indemnitee. 
 (c) If the
determination of entitlement to indemnification is to be made by Independent Counsel pursuant to Section 5(b) hereof, the Independent Counsel shall be selected as provided in this Section 5(c). The Independent Counsel shall
be selected by the Supervisory Board. Indemnitee may, within ten (10) days after such written notice of selection shall have been given, deliver to the Company a written objection to such selection; provided, however, that such objection may be
asserted only on the ground that the Independent Counsel so selected does not meet the requirements of “Independent Counsel” as defined in Section 12 of this Agreement, and the objection shall set forth with particularity the
factual basis of such assertion. Absent a proper and timely objection, the person so selected shall act as Independent Counsel. If a written objection is made and substantiated, the Independent Counsel selected may not serve as Independent
Counsel unless and until such objection is withdrawn or a court has determined that such objection is without merit. If, within twenty (20) days after submission by Indemnitee of a written request for indemnification pursuant to Section
5(a) hereof, no Independent Counsel shall have been selected and not objected to, either the Company or Indemnitee may petition the Dutch court or other court of competent jurisdiction for resolution of any objection which shall have been made
by the Indemnitee to the Company’s selection of Independent Counsel and/or for the appointment as Independent Counsel of a person selected by the court or by such other person as the court shall designate, and the person with respect to whom
all objections are so resolved or the person so appointed shall act as Independent Counsel under Section 5(b) hereof. The Company shall pay any and all reasonable fees and expenses of Independent Counsel incurred by such Independent
Counsel in connection with acting pursuant to Section 5(b) hereof, and the Company shall pay all reasonable fees and expenses incident to the procedures of this Section 5(c), regardless of the manner in which such Independent
Counsel was selected or appointed. 
 (d) In making a determination with respect to entitlement to indemnification hereunder, the person or
persons or entity making such determination shall presume that Indemnitee is entitled to indemnification under this Agreement. Anyone seeking to overcome this presumption shall have the burden of proof and the burden of persuasion by clear and
convincing evidence. Neither the failure of the Company (including by its Supervisory Board members or independent legal counsel) to have made a determination prior to the commencement of any action pursuant to this Agreement that
indemnification is proper in the 

 
circumstances because Indemnitee has met the applicable standard of conduct, nor an actual determination by the Company (including by its Supervisory Board members or independent legal counsel)
that Indemnitee has not met such applicable standard of conduct, shall be a defense to the action or create a presumption that Indemnitee has not met the applicable standard of conduct. 

(e) Indemnitee shall be deemed to have acted in good faith if Indemnitee’s action is based on the records or books of account of the
Enterprise (as hereinafter defined), including financial statements, or on information supplied to Indemnitee by the Management Board members of the Enterprise in the course of their duties, or on the advice of legal counsel for the Enterprise
or on information or records given or reports made to the Enterprise by an independent certified public accountant or by an appraiser or other expert selected with reasonable care by the Enterprise. In addition, the knowledge and/or actions, or
failure to act, of any Supervisory Board member, Management Board member, agent or employee of the Enterprise shall not be imputed to Indemnitee for purposes of determining the right to indemnification under this Agreement. Whether or not the
foregoing provisions of this Section 5(e) are satisfied, it shall in any event be presumed that Indemnitee has at all times acted in good faith and in a manner he reasonably believed to be in or not opposed to the best interests of the
Company. Anyone seeking to overcome this presumption shall have the burden of proof and the burden of persuasion by clear and convincing evidence. 

(f) If the person, persons or entity empowered or selected under Section 5 to determine whether Indemnitee is entitled to
indemnification shall not have made a determination within sixty (60) days after receipt by the Company of the request therefor, the requisite determination of entitlement to indemnification shall be deemed to have been made and Indemnitee shall be
entitled to such indemnification absent (i) a misstatement by Indemnitee of a material fact, or an omission of a material fact necessary to make Indemnitee’s statement not materially misleading, in connection with the request for
indemnification, or (ii) a prohibition of such indemnification under applicable law; provided, however, that such sixty (60)-day period may be extended for a reasonable time, not to exceed an additional thirty (30) days, if the person, persons or
entity making such determination with respect to entitlement to indemnification in good faith requires such additional time to obtain or evaluate documentation and/or information relating thereto; and provided, further, that the foregoing provisions
of this Section 5(f) shall not apply if the determination of entitlement to indemnification is to be made by the shareholders pursuant to Section 5(b) of this Agreement and if (A) within fifteen (15) days after receipt by the Company
of the request for such determination, the Supervisory Board or the Disinterested Supervisory Board members, if appropriate, resolve to submit such determination to the shareholders for their consideration at an annual meeting thereof to be held
within seventy-five (75) days after such receipt and such determination is made thereat, or (B) a special meeting of shareholders is called within fifteen (15) days after such receipt for the purpose of making such determination, such meeting is
held for such purpose within sixty (60) days after having been so called and such determination is made thereat. 
 (g) Indemnitee shall
cooperate with the person, persons or entity making such determination with respect to Indemnitee’s entitlement to indemnification, including providing to such person, persons or entity upon reasonable advance request any documentation or
information which is not privileged or otherwise protected from disclosure and which is reasonably available to Indemnitee and reasonably necessary to such determination. Any Independent Counsel, member of the Supervisory Board or shareholder
of the Company 

 
shall act reasonably and in good faith in making a determination regarding the Indemnitee’s entitlement to indemnification under this Agreement. Any costs or expenses (including
attorneys’ fees and disbursements) incurred by Indemnitee in so cooperating with the person, persons or entity making such determination shall be borne by the Company (irrespective of the determination as to Indemnitee’s entitlement to
indemnification) and the Company hereby indemnifies and agrees to hold Indemnitee harmless therefrom. 
 (h) The Company acknowledges that
a settlement or other disposition short of final judgment may be successful if it permits a party to avoid expense, delay, distraction, disruption and uncertainty. In the event that any action, claim or proceeding to which Indemnitee is a party
is resolved in any manner other than by adverse judgment against Indemnitee (including, without limitation, settlement of such action, claim or proceeding with or without payment of money or other consideration) it shall be presumed that Indemnitee
has been successful on the merits or otherwise in such action, suit or proceeding. Anyone seeking to overcome this presumption shall have the burden of proof and the burden of persuasion by clear and convincing evidence. 

(i) The termination of any Proceeding or of any claim, issue or matter therein, by judgment, order, settlement or conviction, or upon a plea
of nolo contendere or its equivalent, shall not (except as otherwise expressly provided in this Agreement) of itself adversely affect the right of Indemnitee to indemnification or create a presumption that Indemnitee did not act in good faith and in
a manner which he reasonably believed to be in or not opposed to the best interests of the Company or, with respect to any criminal Proceeding, that Indemnitee had reasonable cause to believe that his conduct was unlawful. 

6. Remedies of Indemnitee. 

(a) In the event that (i) a determination is made pursuant to Section 5 of this Agreement that Indemnitee is not entitled to
indemnification under this Agreement, (ii) advancement of Expenses is not timely made pursuant to Section 4 of this Agreement, (iii) no determination of entitlement to indemnification is made pursuant to Section 5(b) of this Agreement
within ninety (90) days after receipt by the Company of the request for indemnification, (iv) payment of indemnification is not made pursuant to this Agreement within ten (10) days after receipt by the Company of a written request therefor or (v)
payment of indemnification is not made within ten (10) days after a determination has been made that Indemnitee is entitled to indemnification or such determination is deemed to have been made pursuant to Section 6 of this Agreement,
Indemnitee shall be entitled to an adjudication in an appropriate court of the Netherlands, or in any other court of competent jurisdiction, of Indemnitee’s entitlement to such indemnification. Indemnitee shall commence such proceeding seeking
an adjudication within one hundred eighty (180) days following the date on which Indemnitee first has the right to commence such proceeding pursuant to this Section 6(a). The Company shall not oppose Indemnitee’s right to seek any
such adjudication. 
 (b) In the event that a determination shall have been made pursuant to Section 5(b) of this Agreement that
Indemnitee is not entitled to indemnification, any judicial proceeding commenced pursuant to this Section 6 shall be conducted in all respects as a de novo trial on the merits, and Indemnitee shall not be prejudiced by reason of the adverse
determination under Section 5(b). 

 (c) If a determination shall have been made pursuant to Section 5(b) of this
Agreement that Indemnitee is entitled to indemnification, the Company shall be bound by such determination in any judicial proceeding commenced pursuant to this Section 6, absent (i) a misstatement by Indemnitee of a material fact, or an
omission of a material fact necessary to make Indemnitee’s misstatement not materially misleading in connection with the application for indemnification, or (ii) a prohibition of such indemnification under applicable law. 

(d) In the event that Indemnitee, pursuant to this Section 6, seeks a judicial adjudication of his rights under, or to recover
damages for breach of, this Agreement, or to recover under any Supervisory Board members’ and Management Board members’ liability insurance policies maintained by the Company, the Company shall pay on his behalf, in advance, any and all
expenses (of the types described in the definition of Expenses in Section 12 of this Agreement) actually and reasonably incurred by him in such judicial adjudication, regardless of whether Indemnitee ultimately is determined to be
entitled to such indemnification, advancement of expenses or insurance recovery. 
 (e) The Company shall be precluded from asserting in
any judicial proceeding commenced pursuant to this Section 6 that the procedures and presumptions of this Agreement are not valid, binding and enforceable and shall stipulate in any such court that the Company is bound by all the
provisions of this Agreement. The Company shall indemnify Indemnitee against any and all Expenses and, if requested by Indemnitee, shall (within ten (10) days after receipt by the Company of a written request therefore) advance, to the extent
not prohibited by law, such expenses to Indemnitee, which are incurred by Indemnitee in connection with any action brought by Indemnitee for indemnification or advance of Expenses from the Company under this Agreement or under any Supervisory Board
members’ and Management Board members’ liability insurance policies maintained by the Company, regardless of whether Indemnitee ultimately is determined to be entitled to such indemnification, advancement of Expenses or insurance recovery,
as the case may be. 
 (f) Notwithstanding anything in this Agreement to the contrary, no determination as to entitlement to
indemnification under this Agreement shall be required to be made prior to the final disposition of the Proceeding. 
 7.
Non-Exclusivity; Survival of Rights; Insurance; Primacy of Indemnification; Subrogation. 
 (a) The rights of indemnification as
provided by this Agreement shall not be deemed exclusive of any other rights to which Indemnitee may at any time be entitled under applicable law, the Articles of Association, any agreement, a vote of shareholders, a resolution of Supervisory Board
members of the Company, or otherwise. No amendment, alteration or repeal of this Agreement or of any provision hereof shall limit or restrict any right of Indemnitee under this Agreement in respect of any action taken or omitted by such
Indemnitee in his Corporate Status prior to such amendment, alteration or repeal. To the extent that a change in applicable law, whether by statute or judicial decision, permits greater indemnification than would be afforded currently
under the Articles of Association and this Agreement, it is the intent of the parties hereto that Indemnitee shall enjoy by this Agreement the greater benefits so afforded by such change. No right or remedy herein conferred is intended to
be exclusive of any other right or remedy, and every other right and remedy shall be cumulative and in addition to every other right and remedy given hereunder or now or hereafter existing at law or in equity or otherwise. The assertion or
employment of any right or remedy hereunder, or otherwise, shall not prevent the concurrent assertion or employment of any other right or remedy. 

 (b) To the extent that the Company maintains an insurance policy or policies providing liability
insurance for Supervisory Board members, Management Board members, employees, or agents or fiduciaries of the Company or of any other corporation, partnership, joint venture, trust, employee benefit plan or other enterprise that such person serves
at the request of the Company, Indemnitee shall be covered by such policy or policies in accordance with its or their terms to the maximum extent of the coverage available for any Supervisory Board member, Management Board member, employee, agent or
fiduciary under such policy or policies. If, at the time of the receipt of a notice of a claim pursuant to the terms hereof, the Company has Supervisory Board members’ and Management Board members’ liability insurance in effect, the
Company shall give prompt notice of the commencement of such proceeding to the insurers in accordance with the procedures set forth in the respective policies. The Company shall thereafter take all necessary or desirable action to cause such
insurers to pay, on behalf of the Indemnitee, all amounts payable as a result of such proceeding in accordance with the terms of such policies. 

(c) In the event of any payment under this Agreement, the Company shall be subrogated to the extent of such payment to all of the rights of
recovery of Indemnitee (other than against the Fund Indemnitors), who shall execute all papers required and take all action necessary to secure such rights, including execution of such documents as are necessary to enable the Company to bring suit
to enforce such rights. 
 (d) The Company shall not be liable under this Agreement to make any payment of amounts otherwise indemnifiable
hereunder if and to the extent that Indemnitee has otherwise actually received such payment under any insurance policy, contract, agreement or otherwise. 

(e) The Company’s obligation to indemnify or advance Expenses hereunder to Indemnitee who is or was serving at the request of the
Company as a Supervisory Board member, Management Board member, employee or agent of any other corporation, partnership, joint venture, trust, employee benefit plan or other enterprise shall be reduced by any amount Indemnitee has actually received
as indemnification or advancement of expenses from such other corporation, partnership, joint venture, trust, employee benefit plan or other enterprise. 

8. Exception to Right of Indemnification. Notwithstanding any provision in this Agreement, the Company shall not be obligated under
this Agreement to make any indemnity in connection with any claim made against Indemnitee: 
 (a) for which payment has actually been made
to or on behalf of Indemnitee under any insurance policy or other indemnity provision, except with respect to any excess beyond the amount paid under any insurance policy or other indemnity provision; or 

(b) for an accounting of profits made from the purchase and sale (or sale and purchase) by Indemnitee of securities of the Company within the
meaning of Section 16(b) of the Securities Exchange Act of 1934, as amended, or similar provisions of Dutch law; or 
 (c) in
connection with any Proceeding (or any part of any Proceeding) initiated by Indemnitee, including any Proceeding (or any part of any Proceeding) initiated by Indemnitee against the Company or its Supervisory Board members, Management Board members,
employees or other indemnitees, unless (i) the Supervisory Board authorized the Proceeding (or any part of any Proceeding) prior to its initiation or (ii) the Company provides the indemnification, in its sole discretion, pursuant to the powers
vested in the Company under applicable law. 

 9. Duration of Agreement. All agreements and obligations of the Company contained
herein shall continue during the period Indemnitee is a member of the Management Board or Supervisory Board member of the Company (or is or was serving at the request of the Company as a Supervisory Board member, Management Board member, employee or
agent of another corporation, partnership, joint venture, trust or other enterprise) and shall continue thereafter so long as Indemnitee shall be subject to any Proceeding (or any proceeding commenced under Section 6 hereof) by reason of
his Corporate Status, whether or not he is acting or serving in any such capacity at the time any liability or expense is incurred for which indemnification can be provided under this Agreement. This Agreement shall be binding upon and inure to
the benefit of and be enforceable by the parties hereto and their respective successors (including any direct or indirect successor by purchase, merger, consolidation or otherwise to all or substantially all of the business or assets of the
Company), assigns, spouses, heirs, executors and personal and legal representatives. 
 10. Security. To the extent requested by
Indemnitee and approved by the Supervisory Board, the Company may at any time and from time to time provide security to Indemnitee for the Company’s obligations hereunder through an irrevocable bank line of credit, funded trust or other
collateral. Any such security, once provided to Indemnitee, may not be revoked or released without the prior written consent of the Indemnitee. 

11. Enforcement. 
 (a)
The Company expressly confirms and agrees that it has entered into this Agreement and assumes the obligations imposed on it hereby in order to induce Indemnitee to serve as a member of the Management Board or Supervisory Board of the Company, and
the Company acknowledges that Indemnitee is relying upon this Agreement in serving as a member of the Management Board or Supervisory Board of the Company. 

(b) This Agreement constitutes the entire agreement between the parties hereto with respect to the subject matter hereof and supersedes all
prior agreements and understandings, oral, written and implied, between the parties hereto with respect to the subject matter hereof. 

(c) The Company shall not seek from a court, or agree to, a “bar order” which would have the effect of prohibiting or
limiting the Indemnitee’s rights to receive advancement of expenses under this Agreement. 

 12. Definitions. For purposes of this Agreement: 

(a) “Corporate Status” describes the status of a person who is or was a Supervisory Board member, Management Board
member, employee, agent or fiduciary of the Company or of any other corporation, partnership, joint venture, trust, employee benefit plan or other enterprise that such person is or was serving at the express written request of the Company. 

(b) “Disinterested Supervisory Board member” means a Supervisory Board member of the Company who is not and was not a
party to the Proceeding in respect of which indemnification is sought by Indemnitee. 
 (c) “Enterprise” shall mean
the Company and any other corporation, partnership, joint venture, trust, employee benefit plan or other enterprise that Indemnitee is or was serving at the express written request of the Company as a Supervisory Board member, Management Board
member, employee, agent or fiduciary. 
 (d) “Expenses” shall include all reasonable attorneys’ fees,
retainers, court costs, transcript costs, fees of experts, witness fees, travel expenses, duplicating costs, printing and binding costs, telephone charges, postage, delivery service fees and all other disbursements or expenses of the types
customarily incurred in connection with prosecuting, defending, preparing to prosecute or defend, investigating, participating, or being or preparing to be a witness in a Proceeding, or responding to, or objecting to, a request to provide discovery
in any Proceeding. Expenses also shall include Expenses incurred in connection with any appeal resulting from any Proceeding and any Dutch or foreign taxes imposed on the Indemnitee as a result of the actual or deemed receipt of any payments under
this Agreement, including without limitation the premium, security for, and other costs relating to any cost bond, supersede as bond, or other appeal bond or its equivalent. Expenses, however, shall not include amounts paid in settlement by
Indemnitee or the amount of judgments or fines against Indemnitee. 
 (e) “Independent Counsel” means a law firm,
or a member of a law firm, that is experienced in matters of corporation law and neither presently is, nor in the past five years has been, retained to represent: (i) the Company or Indemnitee in any matter material to either such party (other than
with respect to matters concerning Indemnitee under this Agreement, or of other indemnitees under similar indemnification agreements), or (ii) any other party to the Proceeding giving rise to a claim for indemnification hereunder. Notwithstanding
the foregoing, the term “Independent Counsel” shall not include any person who, under the applicable standards of professional conduct then prevailing, would have a conflict of interest in representing either the Company or Indemnitee in
an action to determine Indemnitee’s rights under this Agreement. 
 (f) “Proceeding” includes any threatened,
pending or completed action, suit, arbitration, alternate dispute resolution mechanism, investigation, inquiry, administrative hearing or any other actual, threatened or completed proceeding, whether brought by or in the right of the Company or
otherwise and whether civil, criminal, administrative or investigative, in which Indemnitee was, is or will be involved as a party or otherwise, by reason of his or her Corporate Status, by reason of any action taken by him or of any inaction on his
part while acting in his or her Corporate Status; in each case whether or not he is acting or serving in any such capacity at the time any liability or expense is incurred for which indemnification can be provided under this Agreement; including one
pending on or before the date of this Agreement, but excluding one initiated by an Indemnitee pursuant to Section 6 of this Agreement to enforce his rights under this Agreement. 

 13. Severability. The invalidity or unenforceability of any provision hereof shall in
no way affect the validity or enforceability of any other provision. Further, the invalidity or unenforceability of any provision hereof as to either Indemnitee shall in no way affect the validity or enforceability of any provision hereof as to
the other. Without limiting the generality of the foregoing, this Agreement is intended to confer upon Indemnitee indemnification rights to the fullest extent permitted by applicable laws. In the event any provision hereof conflicts with
any applicable law, such provision shall be deemed modified, consistent with the aforementioned intent, to the extent necessary to resolve such conflict. 

14. Modification and Waiver. No supplement, modification, termination or amendment of this Agreement shall be binding unless
executed in writing by both of the parties hereto. No waiver of any of the provisions of this Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a
continuing waiver. 
 15. Notice By Indemnitee. Indemnitee agrees promptly to notify the Company in writing upon being served
with or otherwise receiving any summons, citation, subpoena, complaint, indictment, information or other document relating to any Proceeding or matter which may be subject to indemnification covered hereunder. The failure to so notify the
Company shall not relieve the Company of any obligation which it may have to Indemnitee under this Agreement or otherwise unless and only to the extent that such failure or delay materially prejudices the Company. 

16. Notices. All notices and other communications given or made pursuant to this Agreement shall be in writing and shall be deemed
effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient, and if not so confirmed, then on the next business day,
(c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written
verification of receipt. All communications shall be sent: 
 (a) To Indemnitee at the address set forth below Indemnitee signature
hereto. 
 (b) To the Company at: 

Merus N.V. 
 Padualaan 8
(postvak 133) 
 3584 CH Utrecht, the Netherlands 

Attention: Chief Executive Officer 
 or to such
other address as may have been furnished to Indemnitee by the Company or to the Company by Indemnitee, as the case may be. 
 17.
Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. Counterparts may be delivered via facsimile,
electronic mail (including pdf or any electronic signature complying with the U.S. federal ESIGN Act of 2000, 

 
e.g., www.docusign.com) or any other transmission method and any counterpart so delivered shall be deemed to have been duly and validly delivered and be valid and effective for all
purposes. 
 18. Headings. The headings of the paragraphs of this Agreement are inserted for convenience only and shall not be
deemed to constitute part of this Agreement or to affect the construction thereof. 
 19. Governing law. This Agreement shall be
governed by and construed in accordance with the laws of The Netherlands. 
 20. Dispute resolution. All disputes arising in
connection with this Agreement, or further agreements or contracts resulting thereof, shall in first instance be referred exclusively to the Court of Amsterdam, the Netherlands. 

SIGNATURE PAGE TO FOLLOW 

 IN WITNESS WHEREOF, the parties hereto have executed this Indemnification Agreement on and as of
the day and year first above written. 
  

			
	MERUS N.V.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	
	INDEMNITEE
	
	  

	Name:	 	  

	
	Address:EX-10.9.1

 Exhibit 10.9.1 
  

							
		 	 Rabobank Utrechtse Heuvelrug

Bedrijven
	 	

	  	 Rabobank
  

  

			
	Mailing address	  	P.O. Box 82, 3700 AB Zeist

							
				
		  	Merus B.V.	    	Address	  	Utrechtseweg 25
		  	Mr. T. Logtenberg	    		  	3704 HA Zeist
		  	Padualaan 8	    	Telephone	  	+31 30 221 23 25
		  	P.O. 133	    	Email	  	Bedrijven.uhr@rabobank.nl
		  	3584 CH Utrecht	    	Bank account	  	NL72 RABO 0375 229000
		  		    	Website	  	www.rabobank.nl/uhr

  

			
	Our reference	  	MKB/PH/KG/mg
	Extension	  	+31 30 221 23 25
	Date	  	9 March 2016
		
	Subject	  	Interest option for the next period
		
		  	 Dear Mrs. Margetson and Mr. Logtenberg,
  

Some time ago we have informed you about the lapse of the fixed interest rate period as per 31 March 2016 for your loan with number 3083.901.453. I kindly
request you to make a choice for an interest type and interest rate which shall apply as of 1 April 2016 (effective date).
  

Interest proposal
  

I propose the following interest types and interest rates:
  

•    A fixed interest rate for 1 year as of the effective date: 3.55 % per year. You
will pay the interest in monthly arrears after each month.
  

¡
    A fixed interest rate for 3 years as of the effective date: 3.60% per year. You will pay the interest in monthly arrears after each month.

 
 ¡    A fixed interest rate for 4 years as of the effective date: 3.75% per year. You will pay the interest in monthly arrears
after each month.
  
 ¡    Rabobank Variable Plus Loan. The interest rate is now 4.35% per year. You will pay the
interest in monthly arrears after each month. The bank may amend the interest rate at any time. The terms of this interest type are also stated in the (general) terms and conditions which are applicable to the loan.

 
 I kindly request you to tick the desired interest type and interest rate and to return
this letter duly signed. If I receive this letter by 24 March 2016, your choice shall be effective as of the effective date.
  

Please note: if the above is not met within the proposed time, then from the effective date up to 31 March 2020, the fixed interest rate as offered
in this letter for a period of 4 years shall apply to your loan.
  
 In so far as this
letter does not deviate from the (general) terms and conditions which apply to the loan, the (general) terms and conditions remain applicable.
  

If you have any questions, please do contact me.
  

Best regards,
  

Bedrijven MKB
 for Pieter van Hulsen

 Coöperatieve Rabobank U.A., established in Amsteram 

Registered at the Chamber of Commerce under number 30046259 

					
	Page	  	2/2	  	
	Our reference	  	MKB/PH/KG/mg	  	
		  	  
 Signature(s) for agreement:

 
 Merus B.V.
	  	
			
		  	Place of signature	  	Utrecht
			
		  	Date of signature	  	15/03/2016
			
		  	Legal representative	  	S.J. Margetson
			
		  	Signature	  	/s/ S.J. Margetson
			
		  	Merus B.V.	  	
			
		  	Place of signature	  	Utretcht
			
		  	Date of signature	  	15/03/2016
			
		  	Legal representative	  	T. Logtenberg
			
		  	Signature	  	/s/ T. Logtenberg

  
 Coöperatieve Rabobank U.A., established in
Amsteram 
 Registered at the Chamber of Commerce under number 30046259

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