UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

FLEXION THERAPEUTICS, INC.

(Name of Issuer)

Common Stock, par value $0.001 per share

(Title of Class of Securities)

33938J106

(CUSIP Number)

Thorkil Kastberg Christensen

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)

February 18, 2014

(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 shares of common stock, par value $0.001 per share (the “Common Stock”), of Flexion Therapeutics, Inc., a Delaware corporation (the “Issuer”). The Issuer’s principal executive office is located at 10 Mall Road, Suite 301, Burlington, Massachusetts 01803.

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.

On December 3, 2012, Novo A/S purchased 8,868,393 shares of the Issuer’s then outstanding Series B Preferred Stock, $0.001 par value per share (the “Series B Preferred Stock”), which automatically converted into 1,090,823 shares of the Issuer’s Common Stock (based on a one-for-one conversion ratio and after giving effect to the one-for-8.13 reverse stock split of the Issuer’s Common Stock, which became effective on January 27, 2014) upon the closing of the Issuer’s initial public offering on February 18, 2014 (the “IPO Closing”). The original purchase price per share of Series B Preferred Stock was $1.1275. The purchase price paid by Novo A/S came from its working capital.

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On February 18, 2014, Novo A/S purchased 692,308 shares of the Issuer’s Common Stock from the underwriters in connection with the Issuer’s initial public offering. The purchase price per share of such stock was $13.00. The purchase price paid by Novo A/S came from its working capital.

The acquisitions made by Novo A/S, as described in this Schedule 13D, were for investment purposes only. Novo A/S does not currently have any plans or proposals which relate to or would result in any matters set forth in Items 4(a) through 4(j).

(a) Novo A/S beneficially owns 1,783,131 shares (the “Novo Shares”) of the Issuer’s Common Stock representing approximately 11.42% of the Issuer’s outstanding Common Stock. The percentage of shares owned by Novo A/S is based upon 15,608,014 shares of the Issuer’s Common Stock reported to be outstanding to the reporting person by the Issuer following the closing of the Issuer’s initial public offering on February 18, 2014.

(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 is comprised of Sten Scheibye, Goran Ando, Jorgen Boe, Jeppe Christiansen, Steen Riisgaard and Per Wold-Olsen, and 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 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, any Common Stock of the Issuer held by Novo A/S.

(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 the Novo A/S and reported herein.

(e) Not applicable.

The Issuer, Novo A/S and certain other holders of the Issuer’s securities are party to that certain Amended and Restated Investor Rights Agreement, dated December 3, 2012 (the “Investor Rights Agreement”). The Investor Rights Agreement grants to Novo A/S and the other holders party thereto certain rights, among other things, to (1) cause the Issuer to register with the Securities and Exchange Commission the shares of the Issuer’s Common Stock held by such parties and (2) participate in future registrations of securities by the Issuer, under the circumstances described in the Investor Rights Agreement. If not otherwise exercised, these rights and the underlying agreement will automatically expire and be of no further force or effect three years after the closing of the Issuer’s initial public offering, which occurred on February 18, 2014.

In connection with the Issuer’s initial public offering of Common Stock, Novo A/S entered into a letter agreement (the “Lock-Up Agreement”) with the Issuer and the representatives of the several underwriters for the offering (the “Representatives”), pursuant to which Novo A/S agreed that, during the “Lock-Up Period” as defined below and subject to certain limited exceptions specified in the Lock-Up Agreement, Novo A/S will not (1) offer, pledge, sell,

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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, lend, or otherwise transfer or dispose of, directly or indirectly, any shares of Common Stock or any securities convertible into or exercisable or exchangeable for Common Stock; (2) enter into any swap or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of Common Stock; or (3) publicly disclose the intention to make any such offer, sale, pledge or disposition of shares of Common Stock. In addition, Novo A/S has agreed in the Lock-Up Agreement 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 shares of the Issuer’s capital stock. The “Lock-Up Period” is defined in the Lock-Up Agreement as the period of 180 days after the date of the underwriting agreement executed in connection with the Issuer’s initial public offering of the Common Stock, which was February 18, 2014. 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 Investor 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 Investor 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 Investor Rights Agreement, dated December 3, 2012 (incorporated by reference to Exhibit 4.2 of Flexion Therapeutic, Inc.’s Form S-1 Registration Statement filed January 8, 2014 (File No. 333-193233)).

Exhibit B – Form of Lock-Up Agreement.

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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.

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Exhibit B

Flexion Therapeutics, Inc.

Public Offering of Common Stock

                    , 2014

BMO Capital Markets Corp.

Wells Fargo Securities, LLC

As Representatives of the several Underwriters,

c/o BMO Capital Markets Corp.

3 Times Square, Floor 27

New York, NY 10036

Ladies and Gentlemen:

This letter is being delivered to you in connection with the proposed Underwriting Agreement (the “Underwriting Agreement”), between Flexion Therapeutics, Inc., a Delaware corporation (the “Company”), and each of you as representatives of a group of Underwriters named therein, relating to an underwritten public offering of Common Stock, $0.001 par value (the “Common Stock”), of the Company (the “Offering”).

In order to induce you and the other Underwriters to enter into the Underwriting Agreement, the undersigned will not, without the prior written consent of BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, offer, sell, contract to sell, pledge or otherwise dispose of, (or enter into any transaction which is designed to, or might reasonably be expected to, result in the disposition (whether by actual disposition or effective economic disposition due to cash settlement or otherwise) by the undersigned or any affiliate of the undersigned or any person in privity with the undersigned or any affiliate of the undersigned), directly or indirectly, including the filing (or participation in the filing) of a registration statement with the Securities and Exchange Commission in respect of, or establish or increase a put equivalent position or liquidate or decrease a call equivalent position within the meaning of Section 16 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and the rules and regulations of the Securities and Exchange Commission promulgated thereunder with respect to, any shares of capital stock of the Company or any securities convertible into, or exercisable or exchangeable for such capital stock, or publicly announce an intention to effect any such transaction, for a period from the date hereof until 180 days after the date of the Underwriting Agreement (the “Lock-Up Period”). The foregoing sentence shall not apply to: transfers of shares of Common Stock or any security convertible into Common Stock (i) as a bona fide gift or gifts, or by will or intestate succession upon the death of the undersigned, (ii) to any trust for the direct or indirect benefit of the undersigned or the immediate family of the undersigned, (iii) as a distribution or transfer to: (x) general or limited partners, members, stockholders or affiliates of the undersigned; or (y) any corporation, partnership, limited liability company or other entity which controls or is controlled by the undersigned or to entities under common control with the undersigned, or (iv) with the prior written consent of BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters; provided that in the case of any transfer under

each of clauses (i), (ii) and (iii) it shall be a condition to such transfer that (A) each transferee shall sign and deliver a lock up letter substantially in the form of this lock up letter; (B) any such transfer shall not involve a disposition for value; and (C) no filing under Section 16(a) of the Exchange Act shall be required or shall be voluntarily made during the Lock-up Period. The foregoing restrictions shall also not apply to any shares of Common Stock purchased by the undersigned in the Offering or acquired by the undersigned in the open market after the date of the Underwriting Agreement; provided, however, that no filing under Section 16(a) of the Exchange Act shall be required or shall be voluntarily made during the Lock-Up Period with respect to a sale or other disposition of such shares of Common Stock. If the undersigned is an officer or director of the Company, the undersigned further agrees that the foregoing restrictions shall be equally applicable to any issuer-directed shares of Common Stock the undersigned may purchase in the Offering. For the purposes of this lock-up letter, “immediate family” shall mean the spouse, domestic partner, lineal descendant (including adopted children), father, mother, brother or sister of the undersigned.

Notwithstanding anything herein to the contrary, nothing herein shall prevent (i) the undersigned from establishing a written plan meeting the requirements of Rule 10b5-l (a “10b5-l Plan”) under the Exchange Act, relating to the sale of securities of the Company, provided that (x) the securities subject to such plan may not be sold until after the expiration of the Lock-up Period and (y) that the establishment of such 10b5-l Plan will not result in any public filing or other public announcement of such 10b5-l Plan by the undersigned or the Company during the Lock-up Period, or (ii) the exercise of any options or warrants to purchase capital stock of the Company (including net exercises, through the surrender of shares of Common Stock directly to the Company, to the extent permitted by the instruments representing such options or warrants); provided, however, that in any such case the shares of capital stock issued upon exercise shall remain subject to the provisions of this lock-up letter and no filing under Section 16(a) of the Exchange Act shall be required or shall be voluntarily made during the Lock-Up Period with respect to a sale or other disposition of such shares of Common Stock.

If the undersigned is an officer or director of the Company, (i) BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, 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 shares of Common Stock, they 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 BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, hereunder to any such officer or director shall only be effective two business days after the publication date of such press release. 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 letter 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, BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, waive any prohibition on the transfer of any shares of capital stock of the Company or any securities convertible into, or exercisable or exchangeable for such capital stock, held by any person or entity that beneficially owns 5% or more of the outstanding shares of Common Stock of the Company as of the date of the Underwriting Agreement, BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, shall be deemed to have also waived the prohibitions set forth in this lock-up letter that would otherwise have applied to the undersigned with respect to the same percentage of the undersigned’s shares of Common Stock as the relative percentage of aggregate shares held by such party receiving the waiver which are subject to such waiver. The provisions of this paragraph will not apply unless and until BMO Capital Markets Corp. and Wells Fargo Securities, LLC, as representatives of the several Underwriters, have first waived more than 0.5%, in the aggregate, of the Company’s total outstanding shares of Common Stock from such prohibitions. In the event that, as a result of this paragraph, any shares of capital stock of the Company or any securities convertible into, or exercisable or exchangeable for such capital stock held by the undersigned are released from the restrictions imposed by this lock-up letter, the Company shall notify the undersigned promptly (but in any event within three business days) after becoming aware of any such release; provided that the failure to give such notice shall not give rise to any claim or liability against BMO Capital Markets Corp. and Wells Fargo Securities, LLC or the Underwriters.

The undersigned also agrees and consents to the entry of stop transfer instructions with the Company’s transfer agent and registrar against the transfer of the undersigned’s shares of Common Stock except in compliance with the foregoing restrictions.

With respect to the Offering only, the undersigned waives any registration rights relating to registration under the Securities Act of 1933, as amended, of any shares of capital stock of the Company owned either of record or beneficially by the undersigned, including any rights to receive notice of the Offering or the registration of the Common Stock to be sold in the Offering.

It is understood that, if (i) either the Company notifies BMO Capital Markets Corp. and Wells Fargo Securities, LLC in writing on the one hand, or BMO Capital Markets Corp. and Wells Fargo Securities, LLC notify the Company in writing on the other hand, that it does not intend to proceed with the Offering, (ii) if the Underwriting Agreement is not executed by March 31, 2014; provided, however, that the Company may, by written notice to you prior to March 31, 2014, extend such date for a period of up to an additional 90 days, or (iii) if the Underwriting Agreement (other than the provisions thereof which survive termination) shall terminate or be terminated for any reason prior to payment for and delivery of the shares of Common Stock to be sold in the Offering, this lock-up letter shall immediately be terminated and the undersigned shall automatically be released from all of his, her or its obligations under this lock-up letter.

[Signature page follows]