UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.     )*

Dimension Therapeutics, Inc.

(Name of Issuer)

Common Stock, $0.0001 par value per share

(Title of Class of Securities)

25433V105

(CUSIP Number)

Craig L. Slutzkin

New Leaf Venture Management III, L.L.C.,

Times Square Tower

7 Times Square, Suite 3502

New York, NY 10036

(646) 871-6420

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

October 22, 2015

(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 that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-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 §240.13d-7 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 (“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).

Persons who respond to the collection of information contained in this form are not

required to respond unless the form displays a currently valid OMB control number.

Schedule 13D

Item 1. Security and Issuer.

This statement relates to the Common Stock, $0.0001 par value (the “Common Stock”) of Dimension Therapeutics, Inc. (the “Issuer”) having its principal executive office at 840 Memorial Drive, Cambridge, MA 02139.

Item 2. Identity and Background.

This statement is being filed by:

(a) New Leaf Ventures III, L.P. (“NLV III”) and New Leaf Growth Fund I, L.P. (“NLG I” and, together with NLV III, the “Funds”);

(b) New Leaf Venture Associates III, L.P. (“NLV Associates”), which is the sole general partner of NLV III; New Leaf Growth Associates I, L.P. (“NLG Associates” and, together with NLV Associates, the “GPLPs”), which is the sole general partner of NLG I; and New Leaf Venture Management III, L.L.C. (“NLV Management” and, together with the GPLPs, the “Control Entities”), which is the sole general partner of each of the GPLPs;

(b) Philippe O. Chambon (“Chambon”), Vijay Lathi (“Lathi”), Ronald Hunt (“Hunt”), Jeani Delagardelle (“Delagardelle”) and Liam Ratcliffe (“Ratcliffe” and together with Chambon, Lathi, Hunt and Delagardelle, the “Managing Directors”).

The persons named in this Item 2 are referred to individually herein as a “Reporting Person” and collectively as the “Reporting Persons.”

The address of the principal business office of the Funds, each Control Entity, Chambon, Hunt and Ratcliffe is New Leaf Venture Partners, Times Square Tower, 7 Times Square, Suite 3502, New York, NY 10036. The address of the principal business office of Lathi and Delagardelle is New Leaf Venture Partners, 1200 Park Place, Suite 300, San Mateo, CA 94043.

The principal business of the Funds is to make, hold and dispose of equity and equity-related investments, principally in healthcare, medical device and life sciences companies. The principal business of NLV Associates is to act as the sole general partner of NLV III. The principal business of NLG Associates is to act as the sole general partner of NLG I. The principal business of NLV Management is to act as the sole general partner of the GPLPs. The principal business of each of the Managing Directors is to manage the Control Entities and a number of affiliated partnerships with similar businesses.

During the five years prior to the date hereof, none of the Reporting Persons has been convicted in a criminal proceeding or has been a party to a civil proceeding ending in 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.

Each Fund and each GPLP is a limited partnership organized under the laws of the State of Delaware. NLV Management is a limited liability company organized under the laws of the State of Delaware. Each Managing Director is a citizen of the United States.

Item 3. Source and Amount of Funds or Other Consideration.

On October 21, 2015, the Registration Statement on Form S-1 filed with the Securities and Exchange Commission by the Issuer (File No. 333-206911) in connection with its initial public offering of 5,500,000 shares of Common Stock of the Issuer (the “IPO”) was declared effective.

The closing of the IPO took place on October 22, 2015, and at such closing NLV III purchased an aggregate of 480,769 shares of Common Stock (the “NLV III Securities”) at the IPO price of $13.000 per share. In addition, prior to the IPO, NLV III purchased 2,406,533 shares of Series B Preferred Stock (the “NLV III Series B Stock”) for an aggregate purchase price of $7,749,998.88. Immediately prior to the IPO, the NLV III Series B Stock converted into 823,309 shares of Common Stock of the Issuer. NLV III now holds a total of 1,304,078 shares of the Issuer’s Common Stock (the “NLV III Shares”).

NLG I purchased an aggregate of 480,769 shares of Common Stock (the “NLG I Securities” and, together with the NLV III Securities, the “Securities”), at the IPO price of $13.000 per share. In addition, prior to the IPO, NLG I purchased 802,178 shares of Series B Preferred Stock (the “NLG I Series B Stock”) for an aggregate purchase price of $2,583,334.03. Immediately prior to the IPO, the NLG I Series B stock converted into 274,436 shares of Common Stock of the Issuer. NLG I now holds a total of 755,205 shares of the Issuer’s Common Stock (the “NLG I Shares”).

Collectively, the Funds now hold a total of 2,059,283 shares of the Issuer’s Common stock (the “Firm Shares”).

The working capital of NLV III was the source of the funds for the purchase of the NLV III Securities. The working capital of NLG I was the source of the funds for the purchase of the NLG I Securities. No part of the purchase price of the Securities was represented by funds or other consideration borrowed or otherwise obtained for the purpose of acquiring, holding, trading or voting the Securities.

Item 4. Purpose of Transaction.

The Funds acquired the Common Stock for investment purposes. Depending on market conditions, its continuing evaluation of the business and prospects of the Issuer and other factors, the Funds and other Reporting Persons may dispose of or acquire additional shares of the Issuer. Except as set forth above, none of the Reporting Persons has any present plans which relate to or would result in:

Item 5. Interest in Securities of the Issuer.

By virtue of their relationship as affiliated entities, whose Control Entities have overlapping individual controlling persons, each of the Funds may be deemed to share the power to direct the disposition and vote of the Firm Shares. As the individual managers of NLV Management, each of the Managing Directors also may be deemed to own beneficially the Fund Shares.

Each of the Reporting Persons, except for NLV III and NLG I, disclaims beneficial ownership of the NLV III Shares and NLG I Shares, as applicable, except to the extent of their pecuniary interest therein, if any.

The Percentage of outstanding Common Stock of the Issuer which may be deemed to be beneficially owned by such Reporting Person is set forth on Line 13 of such Reporting Person’s cover sheet. Such percentage was calculated based on the (i) 24,879,574 shares of Common Stock reported to be outstanding on the Issuer’s prospectus filed under Rule 424(b)(4), filed with the Securities and Exchange Commission (the “SEC”) on October 21, 2015 and (ii) 825,000 shares of Common Stock pursuant to the option to the underwriters to purchase up to an aggregate of 825,000 shares of Common Stock within 30 days of October 21, 2015.

Item 6. Contracts, Arrangements, Undertakings or Relationships with Respect to Securities of the Issuer.

The Funds have entered into a lock-up agreement with the representatives of the underwriters of the IPO pursuant to which the Funds have generally agreed, subject to certain exceptions, not to sell any of the Common Stock of the Issuer or any securities convertible into or exercisable or exchangeable for the Common Stock of the Issuer for a period of 180 days from October 21, 2015 without the prior written consent of the representatives of the underwriters.

Item 7. Material to be Filed as Exhibits.

Exhibit 99.1 – Agreement regarding filing of joint Schedule 13D.

Exhibit 99.2 – Powers of Attorney regarding Schedule 13D filings.

SIGNATURE

After reasonable inquiry and to the best of its knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Date: November 2, 2015