SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

SCHEDULE 13D

(Rule 13d-101)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT

TO RULE 13d-2(a)

(Amendment No. 4)*

OvaScience, Inc.

(Name of Issuer)

Common Stock, $0.001 par value per share

(Title of Class of Securities)

69014Q 101

(CUSIP number)

Bessemer Venture Partners

1865 Palmer Avenue, Suite 104

Larchmont, NY 10528

(914) 833-5300

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

January 8, 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 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 §240.13d-7 for other parties to who 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.

* Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

* Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

* Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

* Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

* Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

* Deer Management Co. LLC (“Deer Management”) is the management company affiliate of the Funds (as defined below). An employee of Deer Management, who previously served as the representative of the Funds on the Issuer’s board of directors, was granted stock options as director compensation. As of his resignation date, the number of options noted above had vested. Such employee is contractually obligated to assign to Deer Management any compensation received for his service as a director. See Item 5(c) for further information.

** Calculated based upon 26,580,765 shares of the Issuer’s common stock outstanding after the offering of 2,300,000 shares of the Issuer’s common stock, as reported in the Issuer’s prospectus supplement (to its prospectus dated November 21, 2014), filed on January 8, 2015.

This Amendment No. 4 to Schedule 13D relates to shares of common stock, par value $0.001 per share (the “Shares”), of OvaScience, Inc., a Delaware corporation (the “Issuer”) and amends the Schedule 13D initially filed on February 8, 2013 and as amended on March 21, 2013, May 2, 2013, and December 29, 2014 (collectively, the “Schedule 13D”). Except as set forth herein, the Schedule 13D is unmodified.

Item 2 is hereby amended and restated as follows:

Item 2 (a) – (c). This statement is being filed by the following persons:

Deer Ltd., Deer VII, Bessemer VII, Bessemer VII Institutional, BVP VII SOF and Deer Management are sometimes individually referred to herein as a “Reporting Person” and collectively as the “Reporting Persons.”

Each of the Reporting Persons is principally engaged in the business of investing in securities. The business address and principal executive offices of the each of the Reporting Persons are c/o Bessemer Venture Partners, 1865 Palmer Avenue, Suite 104, Larchmont, NY 10538.

The Shares to which this Schedule 13D relates are owned beneficially by the Funds.

Item 2 (d) – (e). During the last five years, none of the persons identified in this Item 2 has been convicted in any criminal proceeding (excluding traffic violations or similar misdemeanors), or has been a party to any 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 violations with respect to such laws.

Item 2 (f). Each natural person identified in this Item 2 is a citizen of the United States.

No change.

No change.

Item 5 is hereby amended and restated in its entirety as follows:

(a) – (b)

As of January 13, 2015, Bessemer VII, Bessemer VII Institutional and BVP VII had sole voting and dispositive power with respect to 572,463, 253,395 and 977,382 Shares, respectively, representing approximately 2.2%, 1.0% and 3.7% respectively, of the Shares of the Issuer’s common stock outstanding.

As of January 13, 2015, Deer Ltd., through its control of Deer VII, had sole voting and dispositive power with respect to all 1,803,240 Shares beneficially owned by the Funds, representing approximately 6.8% of the Shares of the Issuer’s common stock outstanding.

As of January 13, 2015, Deer VII, through its control of the Funds, had sole voting and dispositive power with respect to all 1,803,240 Shares beneficially owned by the Funds, representing approximately 6.8% of the Shares of the Issuer’s common stock outstanding.

As of January 13, 2015, Deer Management had sole voting and dispositive power with respect to the 7,698 Shares that it beneficially owns, representing approximately 0.0%, of the Shares of the Issuer’s common stock outstanding.

(c) On June 7, 2013, as compensation for service as a director, the Issuer granted Mr. Kraus an option to purchase 4,448 Shares of common stock at $14.00 per Share (the “2013 Option). This option was subject to vesting in twelve equal monthly installments at the end of each successive month following June 7, 2013. On June 13, 2014, as compensation for service as a director, the Issuer granted Mr. Kraus an option to purchase 6,500 Shares of common stock at $8.43 per Share (the “2014 Option”). This option was subject to vesting in twelve equal monthly installments at the end of each successive month following June 13, 2014. Pursuant to the terms of the 2013 Option and 2014 Option agreements, following Mr. Kraus’s resignation from the board on December 23, 2014, his then vested options are exercisable within three months of his resignation date. As of Mr. Kraus’s resignation date, the 2013 Option had fully vested and 3,250 of the 2014 Options had vested. Mr. Kraus is contractually obligated to assign to Deer Management any compensation received for service as a director. As a result, Deer Management currently has the right to acquire a total of 7,698 shares of common stock within three months of December 23, 2014.

During the period from January 7, 2015 to January 13, 2015, the Funds disposed of 515,700 of their Shares in open market transactions through Liquidnet, Inc., a registered broker-dealer. Annex I to this Schedule 13D sets forth a list of these transactions. On January 8, 2015, the cumulative number of Shares sold crossed approximately 1% of the Shares of the Issuer’s common stock outstanding. Therefore, the Reporting Persons are filing this amendment No. 4 to their Schedule 13D.

Except as set forth in Annex I to this Schedule 13D, no Reporting Person has effected any transaction in the Shares of common stock in the last 60 days.

(d) Except as set forth in this Amendment No. 4 to Schedule 13D, to the knowledge of the Reporting Persons, no person had the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, securities covered by this Amendment No. 4 to Schedule 13D.

(e) Not applicable.

No change.

No change.

Annex I

Information With Respect to Transactions of Shares during the Past 60 Days⁽¹⁾

Bessemer Venture Partners VII L.P.

Bessemer Venture Partners VII Institutional L.P.

BVP VII Special Opportunity Fund L.P.

SIGNATURES

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

Dated: January 13, 2015