UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

Information To Be Included in Statements Filed Pursuant to § 240.13d-1(a) and

Amendments Thereto Filed Pursuant to § 240.13d-2(a)

(Amendment No. 3)*

WAVE Life Sciences Ltd.

(Name of Issuer)

Ordinary Shares

(Title of Class of Securities)

Y95308105

(CUSIP Number)

Ken Takanashi

St. Luke’s Tower 12F, 8-1, Akashi-cho, Chuo-ku,

Tokyo 104-0044, Japan

+81-3-5565-6148

(Name, Address and Telephone Number of Person

Authorized to Receive Notices and Communications)

With Copies To:

Morgan, Lewis & Bockius LLP

ATTN: Bradley K. Edmister

101 Park Avenue, New York, New York 10178-0060

Telephone: +1-212-309-6110

March 19, 2018

(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 off §§ 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).

This Amendment No. 3 amends the Schedule 13D filed with the Securities and Exchange Commission on November 25, 2015, as previously amended from time to time (the “Schedule 13D”). Unless otherwise stated herein, the Schedule 13D remains in full force and effect. Terms used herein and not otherwise defined herein shall have the meaning ascribed thereto in the Schedule 13D.

Item 5. Interest in Securities of the Issuer

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

The information in this Item 5(a) and in Row 13 of each cover page to this Schedule 13D with respect to SNBL, Mr. Takanashi and SNBL USA is based on an aggregate of 27,992,244 shares of the Issuer’s Ordinary Shares issued and outstanding as of March 1, 2018, as reported in the Issuer’s Annual Report on Form 10-K for the year ended December 31, 2017, filed with the SEC on March 12, 2018.

(a) SNBL may be deemed to beneficially own 5,885,478 of the Issuer’s Ordinary Shares, representing 21.0% of the Issuer’s issued and outstanding shares and consisting of (i) 1,697,467 Ordinary Shares held by SNBL; (ii) 286,663 Ordinary Shares held by SNBL USA; (iii) 1,801,348 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL; and (iv) 2,100,000 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL USA.

Mr. Takanashi may be deemed to beneficially own 5,894,478 of the Issuer’s Ordinary Shares, representing 21.1% of the Issuer’s issued and outstanding shares and consisting of (i) 1,697,467 Ordinary Shares held by SNBL; (ii) 286,663 Ordinary Shares held by SNBL USA; (iii) 1,801,348 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL; (iv) 2,100,000 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL USA; and (v) 9,000 Ordinary Shares underlying options exercisable within 60 days of April 2, 2018 held by Mr. Takanashi.

SNBL USA may be deemed to beneficially own 2,386,663 of the Issuer’s Ordinary Shares, representing 8.5% of the Issuer’s issued and outstanding shares and consisting of 286,663 Ordinary Shares held by SNBL USA and 2,100,000 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL USA.

Each of the Reporting Persons expressly disclaims beneficial ownership of the securities of the Issuer owned by all other Reporting Persons except to the extent of its or his pecuniary interest therein.

(b) SNBL and Mr. Takanashi share the power to vote or dispose of the: (i) 1,697,467 Ordinary Shares held by SNBL; (ii) 286,663 Ordinary Shares held by SNBL USA; (iii) 1,801,348 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL; and (iv) 2,100,000 Ordinary Shares underlying immediately convertible Series A preferred shares held by SNBL USA.

SNBL USA shares the power to vote or dispose of the 286,663 Ordinary Shares it holds and the 2,100,000 Ordinary Shares underlying immediately convertible Series A preferred shares it holds.

(c) On November 16, 2015, in connection with the closing of the IPO, SNBL USA purchased 125,000 of the Issuer’s Ordinary Shares at $16 per share.

(d) No other person is known to have the right to receive, or the power to direct the receipt of dividends from, any proceeds from the sale of the Ordinary Shares of the Issuer beneficially owned by any of the Reporting Persons.

(e) Not applicable.

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

Item 6 is hereby amended and supplemented by adding the following:

March 19 Share Transfer Agreement

SNBL and SNBL USA entered into a Share Transfer Agreement, dated March 19, 2018 (the “March 19 Share Transfer Agreement”) whereby SNBL transferred immediately convertible Series A preferred shares representing 2,100,000 Ordinary Shares to SNBL USA.

The foregoing description of the March 19 Share Transfer Agreement is qualified in its entirety by reference to the full text of the March 19 Share Transfer Agreement, which is filed herewith as Exhibit 99.8.

December 28 Stock Pledge Agreement

Pursuant to a Stock Pledge Agreement, dated December 28, 2016 (the “December 28 Stock Pledge Agreement”), SNBL USA has pledged 286,663 Ordinary Shares for the benefit of The Kagoshima Bank, Ltd. (the “Kagoshima Bank”) in order to secure the obligations of SNBL under a loan agreement, dated December 28, 2016, between SNBL and Kagoshima Bank.

The foregoing description of the December 28 Stock Pledge Agreement is qualified in its entirety by reference to the full text of the December 28 Stock Pledge Agreement, which is filed herewith as Exhibit 99.9.

Amendment to December 28 Pledge Agreement

Pursuant to the Amendment to Pledge Agreement, dated as of June 30, 2017 (the “Amendment to December 28 Pledge Agreement”), to the December 28 Stock Pledge Agreement, dated as of December 28, 2016, between SNBL USA and Kagoshima Bank, the secured obligations under the December 28 Stock Pledge Agreement were amended to include a new loan from Kagoshima Bank to SNBL in the principal amount of ¥600,000,000 made pursuant to a loan agreement, dated as of June 30, 2017, between SNBL and Kagoshima Bank.

The foregoing description of the Amendment to December 28 Pledge Agreement is qualified in its entirety by reference to the full text of the Amendment to December 28 Pledge Agreement, which is filed herewith as Exhibit 99.10.

Second Amendment to December 28 Pledge Agreement

Pursuant to the Second Amendment to Pledge Agreement, dated as of December 27, 2017 (the “Second Amendment to December 28 Pledge Agreement”), to the December 28 Stock Pledge Agreement and Amendment to December 28 Pledge Agreement, dated as of December 28, 2016 and June 30, 2017, respectively, between SNBL USA and Kagoshima Bank, the secured obligations under the December 28 Stock Pledge Agreement and the Amendment to December 28 Pledge Agreement were amended to include a new loan from Kagoshima Bank to SNBL in the principal amount of ¥600,000,000 made pursuant to a loan agreement, dated as of December 27, 2017, between SNBL and Kagoshima Bank.

The foregoing description of the Second Amendment to December 28 Pledge Agreement is qualified in its entirety by reference to the full text of the Second Amendment to December 28 Pledge Agreement, which is filed herewith as Exhibit 99.11.

Kagoshima Bank Deed of Charge of Shares

SNBL and Kagoshima Bank entered into a Deed of Charge of Shares, dated September 15, 2017 (the “Kagoshima Bank Deed of Charge of Shares”) whereby SNBL has pledged 915,464 Ordinary Shares for the benefit of Kagoshima Bank in order to secure the obligations of SNBL under a loan agreement, dated September 23, 2016, between SNBL and Kagoshima Bank.

The foregoing description of the Kagoshima Bank Deed of Charge of Shares is qualified in its entirety by reference to the full text of the Kagoshima Bank Deed of Charge of Shares, which is filed herewith as Exhibit 99.12.

Syndication Deed of Charge of Shares

SNBL, Kagoshima Bank and the Lenders (as defined in the Deed of Charge of Shares, dated September 15, 2017 (the “Syndication Deed of Charge of Shares”), which is filed herewith as Exhibit 99.13), entered into the Syndication Deed of Charge of Shares whereby SNBL has pledged 720,063 Ordinary Shares for the benefit of the Lenders in order to secure the obligations of SNBL under a loan agreement, dated September 15, 2017, between SNBL and the Lenders.

The foregoing description of the Syndication Deed of Charge of Shares is qualified in its entirety by reference to the full text of the Syndication Deed of Charge of Shares, which is filed herewith as Exhibit 99.13.

Item 7. Materials to Be Filed as Exhibits

Item 7 is hereby amended and supplemented by adding the following:

Exhibit 99.8: March 19 Share Transfer Agreement, dated March 19, 2018, by and between SNBL and SNBL USA.

Exhibit 99.9: December 28 Stock Pledge Agreement, dated December 28, 2016, by and between SNBL USA and Kagoshima Bank.

Exhibit 99.10: Amendment to December 28 Pledge Agreement, dated June 30, 2017, by and between SNBL USA and Kagoshima Bank.

Exhibit 99.11: Second Amendment to December 28 Pledge Agreement, dated December 27, 2017, by and between SNBL USA and Kagoshima Bank.

Exhibit 99.12: Kagoshima Bank Deed of Charge of Shares, dated September 15, 2017, by and between SNBL and Kagoshima Bank.

Exhibit 99.13: Syndication Deed of Charge of Shares, dated September 15, 2017, by and between SNBL, Kagoshima Bank and the Lenders.

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SIGNATURE

After reasonable inquiry and to the best of the knowledge and belief, the undersigned certify that the information set forth in this Amendment No. 3 is true, complete and correct.

April 26, 2018

SCHEDULE 1

The following table sets forth the name and present principal occupation or employment, for each executive officer and director of Shin Nippon Biomedical Laboratories, Ltd. Each of the executive officers and directors of Shin Nippon Biomedical Laboratories, Ltd. listed below is a citizen of Japan.

Shin Nippon Biomedical Laboratories, Ltd.

SCHEDULE 2

The following table sets forth the name and present principal occupation or employment, for each executive officer and director of SNBL USA, Ltd. Each of the executive officers and directors of SNBL USA, Ltd. listed below is a citizen of Japan.

SNBL USA, Ltd.