UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

Ra Pharmaceuticals, Inc.

(Name of Issuer)

Common Stock

(Title of Class of Securities)

74933V 10 8

(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)

October 31, 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).

This Schedule 13D relates to the common stock, par value $0.001 per share (the “Common Stock”), of Ra Pharmaceuticals, Inc. (the “Issuer”), a Delaware corporation. The Issuer’s principal office is located at 87 Cambridge Park Drive, Cambridge, Massachusetts 02140.

(a)    The reporting person (“Reporting Person”) is Novo A/S, a Danish limited liability company that is wholly owned by Novo Nordisk Fonden (the “Foundation”), a Danish commercial foundation. Novo A/S is the holding company in the group of Novo companies (currently comprised of Novo Nordisk A/S, Novozymes A/S and NNIT A/S) and is responsible for managing the Foundation’s assets, including its financial assets. Based on the governance structure of Novo A/S and the Foundation, the Foundation is not deemed to have any beneficial ownership of the securities of the Issuer held by Novo A/S. 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.

(b)    The business address of both Novo A/S and the Foundation is Tuborg Havnevej 19, 2900 Hellerup, Denmark. 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.

(c)    Novo A/S, a holding company that is responsible for managing the Foundation’s assets, provides seed and venture capital to development stage companies and invests in well-established companies within the life science and biotechnology sector. 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.

(d)    Within the last five years, neither Novo A/S, the Foundation, nor any person named in Schedule I has been convicted in any criminal proceedings.

(e)    Within the last five years, neither Novo A/S, the Foundation, nor any person named in Schedule I was a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Prior to the Issuer’s initial public offering (the “IPO”), the Reporting Person held Series B-1 and Series B-2 Preferred Stock (the “Preferred Stock”) of the Issuer as set forth under Column E in the table below. On October 31, 2016 (the “IPO Closing Date”), (i) the Preferred Stock automatically converted (after giving effect to a 1-for-7 reverse stock split effected by the Issuer on October 14, 2016) on a one-for-one basis for no additional consideration into 1,785,408 shares of Common Stock and (ii) the Reporting Person purchased 246,154 shares of Common Stock from the underwriters (the “IPO Shares”) pursuant to the provisions of the Underwriting Agreement among the Issuer and the several underwriters for the offering (the “Underwriters”), resulting in an aggregate of 2,031,562 shares of Common Stock as set forth under Column F.

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. Peter Tuxen Bisgaard, a member of the board of directors of the Issuer, is employed as a Partner of Novo Ventures (US), Inc. Mr. Bisgaard 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 2,031,562 shares of Common Stock (the “Novo Shares”), representing approximately 9.5% of the Issuer’s outstanding Common Stock, based upon 21,488,780 shares of Common Stock (assuming no exercise of the underwriters’ option to purchase additional shares of common stock) 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 October 26, 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. Peter Tuxen Bisgaard, a member of the board of directors of the Issuer, is employed as a Partner of Novo Ventures (US), Inc. Mr. Bisgaard 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 Stock 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 Stock 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 Stock held in the name of Novo A/S and reported herein.

(e)    Not applicable.

Amended and Restated Investors’ Rights Agreement

The Issuer, Novo A/S and certain other holders of the Issuer’s securities are party to that certain Amended and Restated Investors’ Rights Agreement dated as of July 10, 2015 (the “Rights Agreement”). The Rights Agreement grants to Novo A/S and the other parties thereto certain rights that include demand registration rights, piggyback registration rights and Form S-3 registration rights as more fully described in such agreement which will expire, with respect to any particular stockholder, upon the earlier of: (i) a Deemed Liquidation Event (as defined therein), (ii) five (5) years after the closing of the IPO or (iii) at such time following the Issuer’s IPO when a holder holds less than one percent (1%) of the outstanding securities of the Issuer and all Registrable Securities (as defined therein) of such holder may be sold without restriction pursuant to Rule 144 of the Securities Act of 1933, as amended, within a three (3) month period.

Lock-Up Agreement

Novo A/S entered into a letter agreement with the Issuer and the Underwriters, on August 17, 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 Stock or such other securities for a period of 180 days after the date of the Underwriting Agreement among the Issuer and the Underwriters. 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 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 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: Amended and Restated Investors’ Rights Agreement (incorporated by reference to Exhibit 4.1 of Form S-1 Registration Statement of the Issuer filed with the Securities and Exchange Commission on September 30, 2016 (File No. 333-213917)).

Exhibit B: Lock-Up Agreement dated August 17, 2016 between Novo A/S and the Underwriters.

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.

EXHIBIT B

August 17, 2016

Ra Pharmaceuticals, Inc.

87 Cambridge Park Dr.

Cambridge, MA 02140

Credit Suisse Securities (USA) LLC

Jefferies LLC

BMO Capital Markets Corp.

As Representatives of the several Underwriters

Eleven Madison Avenue

New York, NY 10010

520 Madison Avenue

New York, NY 10022

3 Times Square, 25th Floor

New York, NY 10036

Dear Sir or Madam:

As an inducement to the Underwriters to execute the Underwriting Agreement (the “Underwriting Agreement”), pursuant to which an offering (the “Public Offering”) will be made that is intended to result in the establishment of a public market for the common stock, $0.001 par value per share (the “Securities”) of Ra Pharmaceuticals, Inc., a Delaware corporation, and any successor (by merger or otherwise) thereto, (the “Company”), the undersigned hereby agrees that during the period specified in the following paragraph (the “Lock-Up Period”), the undersigned will not offer, sell, contract to sell, pledge or otherwise dispose of, directly or indirectly, any Securities or securities convertible into or exchangeable or exercisable for any Securities, enter into a transaction which would have the same effect (each, a “Transaction”), or enter into any swap, hedge or other arrangement that transfers, in whole or in part, any of the economic consequences of ownership of the Securities, whether any such aforementioned transaction is to be settled by delivery of the Securities or such other securities, in cash or otherwise (each, a “Swap”), or publicly disclose the intention to make any such offer, sale, pledge or disposition, or to enter into any such transaction, swap, hedge or other arrangement, without, in each case, the prior written consent of Credit Suisse Securities (USA) LLC, Jefferies LLC and BMO Capital Markets Corp., as representatives of the several Underwriters (collectively, the “Representatives”). In addition, the undersigned agrees that, without the prior written consent of the Representatives, it will not, during the Lock-Up Period, make any demand for or exercise any right with respect to, the registration of any Securities or any security convertible into or exercisable or exchangeable for the Securities; provided, that if the Company first receives a waiver to sell Lock-Up Securities (as defined in the Underwriting Agreement) pursuant to a registered offering on Form S-1 during the Lock-Up Period, the forepart of this sentence shall not operate as a prohibition, other than in respect of the Public Offering, of the undersigned’s piggyback registration rights pursuant to Section 2.2 of that certain Amended and Restated Investor Rights Agreement, dated July 10, 2015 (the “IRA”), between the Company and the undersigned, during the Lock-Up Period; provided, further, that the undersigned may not participate in any such public offering without first obtaining a release from the terms hereof from the Representatives.

The initial Lock-Up Period will commence on the date of this Lock-Up Agreement and include the date that is 180 days after the public offering date set forth on the final prospectus used to sell the Securities (the “Public Offering Date”) pursuant to the Underwriting Agreement, to which you are or expect to become parties.

Any Securities received upon exercise of options granted or warrants issued to the undersigned will also be subject to this Lock-Up Agreement.

Notwithstanding anything herein to the contrary, the restrictions contained in this letter agreement (this “Lock-Up Agreement”) shall not apply to any of the following: (i) transfers of Securities as a bona fide gift or gifts or for bona fide estate planning purposes; (ii) transfers of Securities or other securities of the Company to a trust or limited family partnership for the direct or indirect benefit of the undersigned or the immediate family of the undersigned (for purposes of this Lock-Up Agreement, “immediate family” shall mean any relationship by blood, current or former marriage or adoption, not more remote than first cousin); (iii) transfers of Securities or other securities of the Company by will, other testamentary document or intestate succession in a transaction not involving a disposition for value; (iv) transfers of Securities or other securities of the Company pursuant to a court order in respect of, or by operation of law as a result of, a divorce, in a transaction not involving a disposition for value; (v) the transfer of Securities to the Company in connection with the exercise, including by and to the extent necessary to cover any “net” exercise, of any options or warrants to acquire Securities or the conversion of any convertible security into Securities in accordance with its terms, provided that any Securities issued to the undersigned upon such exercise or conversion shall be subject to the restrictions set forth herein and no filing or public announcement by any party under the Securities Exchange Act of 1934 (the “Exchange Act”) or otherwise shall be required or shall be voluntarily made in connection with such transfer, exercise, or conversion (other than a filing on a Form 5 made after the expiration of the Lock-Up Period or, in the case of a “net” exercise, a filing on a Form 4 that reports such “net” exercise under the transaction code “F”); (vi) transfers of Securities or other securities of the Company to a limited liability company or partnership wholly-owned and controlled by the undersigned, provided that the transfer shall not involve a disposition for value; (vii) if the undersigned is a trust, transfers of Securities or other securities of the Company to any beneficiary of the undersigned or the estate of any such beneficiary, provided that the transfer shall not involve a disposition for value; (viii) transfers or distributions of Securities to members, limited partners, stockholders or affiliates of, or any investment fund or other entity that controls or manages, the undersigned (including, for the avoidance of doubt, a fund controlled by or under common control with the same manager or managing member or general partner or management company or by an entity controlling, controlled by, or under common control with such manager or managing member or general partner or management company as the undersigned or who shares a common controlling investment advisor with the undersigned), provided that the transfer or distribution shall not involve a disposition for value; (ix) transfers or distributions in connection with a merger or sale of all or substantially all of the voting securities or assets of the Company, regardless of how such a transaction is structured (it being further understood that this agreement shall not restrict the undersigned from entering into any agreement or arrangement in connection therewith, including an agreement to vote in favor of, or tender Securities or other securities of the Company in, any such transaction or taking any other action in connection with any such transaction), provided that the restrictions set forth herein shall continue to apply should the completion of the transaction not occur; (x) the entering into by the undersigned of a written trading plan pursuant to Rule 10b5-1 of the Exchange Act during the Lock-Up Period, provided that no sales of the undersigned’s Securities shall be made pursuant to such plan, and no public disclosures shall be made regarding such plan, prior to the expiration of the Lock-Up Period; or (xi) Securities purchased by the undersigned in the open market or in the Public Offering, including any issuer directed share program, provided that no filing or public announcement by any party under Section 16 of the Exchange Act shall be required or shall be voluntarily made in connection with such Transaction or Swap (other than a filing on a Form 5 made after the expiration of the Lock-Up Period); provided further that, with respect to clauses (i), (ii), (iii), (iv), (vi), (vii) and (viii), (a) each transferee or distributee agrees to be bound in writing by the terms of this Lock-Up Agreement prior to such transfer, and (b) no filing or public announcement by any party under the Exchange Act or otherwise shall be required or shall be voluntarily made in connection with such transfer, exercise, conversion or distribution (other than a filing on a Form 5 made after the expiration of the Lock-Up Period).

In furtherance of the foregoing, the Company and its transfer agent and registrar are hereby authorized to decline to make any transfer of shares of Securities if such transfer would constitute a violation or breach of this Lock-Up Agreement.

If the undersigned is an officer or director of the Company, the undersigned further agrees that the foregoing restrictions in this Lock-Up Agreement shall be equally applicable to any issuer-directed Securities the undersigned may purchase in the above-referenced offering.

If the undersigned is an officer or director of the Company, (i) the Representatives agree that, at least three business days before the effective date of any release or waiver of the foregoing restrictions in connection with a transfer of Securities, the Representatives will notify the Company of the impending release or waiver, and (ii) the Company has agreed in the Underwriting Agreement to announce the impending release or waiver by press release through a major news service at least two business days before the effective date of the release or waiver. Any release or waiver granted by the Representatives hereunder to any such officer or director shall only be effective two business days after the date of such publication. The provisions of this paragraph will not apply if (a) the release or waiver is effected solely to permit a transfer not for consideration and (b) the transferee has agreed in writing to be bound by the same terms described in this Lock-Up Agreement to the extent and for the duration that such terms remain in effect at the time of the transfer.

In the event that, during the Lock-Up Period, the Representatives waive any prohibition on the transfer of any Securities held by any executive officer or director of the Company or any holder of more than 2.5% of the outstanding Common Stock of the Company on a fully-diluted basis that is subject to a lock-up agreement related to the Public Offering similar in terms or form to this Lock-up Agreement, then the Representatives shall be deemed to have also waived, on the same terms, the prohibitions set forth in this Lock-Up Agreement that would otherwise have applied to the undersigned on a pro-rata basis with respect to the same proportion of the undersigned’s Securities subject to this Lock-Up Agreement as (x) the aggregate Securities held by such party receiving the waiver that is subject to the waiver bears to (y) the aggregate Securities held by such party that is subject to a lock-up agreement related to the Public Offering similar in terms or form to this Lock-Up Agreement. The provisions of this paragraph will not apply: (i) unless and until the Representatives have first waived more than two and one-half percent (2.5%) of the Company’s total outstanding Securities (determined as of the Public Offering Date for, and giving effect to, the Public Offering) from such prohibitions, (ii) (a) if the release or waiver is effected solely to permit a transfer not involving a disposition for value and (b) the transferee has agreed in writing to be bound by the same terms described in this Lock-Up Agreement to the extent and for the duration that such terms remain in effect at the time of the transfer, or (iii) if the release or waiver is granted to a holder of Securities in connection with an underwritten public offering during the Lock-Up Period, whether or not such offering is wholly or partially a secondary offering, of Securities pursuant to a registration statement under the Securities Act of 1933, as amended; provided that the participants are offered the opportunity to participate in the offering on a basis consistent with such contractual rights in the IRA. In the event that any percentage of such Securities released from the restrictions set forth in this Lock-Up Agreement are subject to any restrictions of the type set forth in this Lock-Up Agreement, the same restrictions shall be applicable to the release of the same percentage of the undersigned’s Securities. In the event that, as a result of this paragraph, any Securities held by the undersigned are released from the restrictions imposed by this Lock-Up Agreement, the Representatives shall use commercially reasonable efforts to notify the Company within two business days of the effective date of such release (it being understood and agreed that the failure to give such notice to the Company shall not give rise to any claim or liability against the Representatives).

This Lock-Up Agreement shall be binding on the undersigned and the successors, heirs, personal representatives and assigns of the undersigned. This Lock-Up Agreement shall lapse and become null and void upon the earliest to occur, if any, of (i) if the Public Offering Date shall not have occurred on or before May 15, 2017, (ii) the Company filing an application with the Securities and Exchange Commission to withdraw the registration statement related to the Public Offering, (iii) the date on which the Underwriting Agreement (other than the provisions thereof which survive termination) shall terminate or be terminated prior to payment for and delivery of the Securities to be sold thereunder, or (iv) upon written notice from an authorized officer of the Company to the Representatives, executed or delivered prior to the signing of the Underwriting Agreement, that the Company has determined not to proceed with the public offering of the Securities. This agreement shall be governed by, and construed in accordance with, the laws of the State of New York.