Exhibit 4.1



ZQ|CERT#|COY|CLS|RGSTRY|ACCT#|TRANSTYPE|RUN#|TRANS#   . COMMON STOCK PAR VALUE $0.001 COMMON STOCK THIS CERTIFICATE IS TRANSFERABLE   IN CANTON, MA, JERSEY CITY, NJ AND COLLEGE STATION, TX Shares * * 000000 * *   * * * * * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * * *   * * * * * 000000 * * * * * * * * * * * * * * * * * * * * * 000000 * * * * * *   * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * Certificate   Number ZQ00000000 VOYAGER THERAPEUTICS, INC. INCORPORATED UNDER THE LAWS OF   THE STATE OF DELAWARE ** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David THIS CERTIFIES THAT Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander Alexander David SamMple ***R*   Mr. A.lexaSnderADavidMSampPle ***L* MrE. Alexan&der DavMid SamRple **S**   Mr.. AleSxandeAr DaMvid SamPple *L*** MEr. Alex&ander David Sample ****   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   Sample **** Mr. AlexandeMr DaviRd Sam.ple S**** MAr. AleMxandePr DavLid   SEample *&*** Mr. AMlexanRder DaSvid S.ampSle ***A* Mr.MAlexanPder   DLavidESample **** Mr. Alexander **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David SEE REVERSE FOR CERTAIN DEFINITIONS David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Sample **** Mr. Sample   is the owner of   **000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares***   *000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****   000000**Shar*es****0*000Z00**SEhareRs****00O0000**ShHares**U**0000N00**SDhares*R***000E000**DShares**T**000H000**SOhares*U***000S000**AShareNs****00D0000**Shares****0   00000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****00   0000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000   000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****0000   00**Shares****0Z0000E0**ShRares***O*000000*H*ShareUs****0N00000D**SharRes****0E0000D0**ShareAs****0N00000D**SharesZ****00E0000R**SharOes****0*000*00**Shares****00000   0**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000   **Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000*   *Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**   Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**S   FULLY-PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK OF Voyager Therapeutics,   Inc. (hereinafter called the “Voyager Therapeutics, Inc.”), transferable on   the books of the Voyager Therapeutics, Inc. in person or by duly authorized   attorney, upon surrender of this Certificate properly endorsed. This   Certificate and the shares represented hereby, are issued and shall be held   subject to all of the provisions of the Articles of Incorporation, as   amended, and the By-Laws, as amended, of the Voyager Therapeutics, Inc.   (copies of which are on file with the Voyager Therapeutics, Inc. and with the   Transfer Agent), to all of which each holder, by acceptance hereof, assents.   This Certificate is not valid unless countersigned and registered by the   Transfer Agent and Registrar. Witness the facsimile seal of the Voyager   Therapeutics, Inc. and the facsimile signatures of its duly authorized   officers. DATED DD-MMM-YYYY COUNTERSIGNED AND REGISTERED: COMPUTERSHARE TRUST   COMPANY, N.A. TRANSFER AGENT AND REGISTRAR, President and CEO 2013 DELAWARE   By Senior V.P. Finance and Business Development AUTHORIZED SIGNATURE CUSIP   Holder ID Insurance Value Number of Shares DTC Certificate Numbers   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890 Total   Transaction XXXXXX XX X XXXXXXXXXX 1,000,000.00 123456 12345678 123456789012345   Voyager Therapeutics, Inc. PO BOX 43004, Providence, RI 02940-3004 Num/No.   Denom. Total 1 2 3 4 5 6 7 1 2 3 4 5 6 1 2 3 4 5 6 MR A SAMPLE DESIGNATION   (IF ANY) ADD 1 ADD 2 ADD 3 ADD 4 O CUSIP XXXXXX XX X 


    




 










. VOYAGER   THERAPEUTICS, INC. THE COMPANY WILL FURNISH WITHOUT CHARGE TO EACH   SHAREHOLDER WHO SO REQUESTS, A SUMMARY OF THE POWERS, DESIGNATIONS,   PREFERENCES AND RELATIVE, PARTICIPATING, OPTIONAL OR OTHER SPECIAL RIGHTS OF   EACH CLASS OF STOCK OF THE COMPANY AND THE QUALIFICATIONS, LIMITATIONS OR   RESTRICTIONS OF SUCH PREFERENCES AND RIGHTS, AND THE VARIATIONS IN RIGHTS,   PREFERENCES AND LIMITATIONS DETERMINED FOR EACH SERIES, WHICH ARE FIXED BY   THE ARTICLES OF INCORPORATION OF THE COMPANY, AS AMENDED, AND THE RESOLUTIONS   OF THE BOARD OF DIRECTORS OF THE COMPANY, AND THE AUTHORITY OF THE BOARD OF   DIRECTORS TO DETERMINE VARIATIONS FOR FUTURE SERIES. SUCH REQUEST MAY BE MADE   TO THE OFFICE OF THE SECRETARY OF THE COMPANY OR TO THE TRANSFER AGENT. THE   BOARD OF DIRECTORS MAY REQUIRE THE OWNER OF A LOST OR DESTROYED STOCK   CERTIFICATE, OR HIS LEGAL REPRESENTATIVES, TO GIVE THE COMPANY A BOND TO   INDEMNIFY IT AND ITS TRANSFER AGENTS AND REGISTRARS AGAINST ANY CLAIM THAT   MAY BE MADE AGAINST THEM ON ACCOUNT OF THE ALLEGED LOSS OR DESTRUCTION OF ANY   SUCH CERTIFICATE. (Cust) (Minor) (State) (Cust) and not as tenants in common   (Minor) (State) PLEASE INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF   ASSIGNEE For value received, hereby sell, assign and transfer unto (PLEASE   PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING POSTAL ZIP CODE, OF ASSIGNEE)   Shares of the common stock represented by the within Certificate, and do   hereby irrevocably constitute and appoint Attorney to transfer the said stock   on the books of the within-named Company with full power of substitution in   the premises. Dated: 20 Signature: Signature: Notice: The signature to this   assignment must correspond with the name as written upon the face of the   certificate, in every particular, without alteration or enlargement, or any change   whatever. The IRS requires that we report the cost basis of certain shares   acquired after January 1, 2011. If your shares were covered by the   legislation and you have sold or transferred the shares and requested a   specific cost basis calculation method, we have processed as requested. If   you did not specify a cost basis calculation method, we have defaulted to the   first in, first out (FIFO) method. Please visit our website or consult your   tax advisor if you need additional information about cost basis. If you do   not keep in contact with us or do not have any activity in your account for   the time periods specified by state law, your property could become subject   to state unclaimed property laws and transferred to the appropriate state.   Signature(s) Guaranteed: Medallion Guarantee Stamp THE SIGNATURE(S) SHOULD BE   GUARANTEED BY AN ELIGIBLE GUARANTOR INSTITUTION (Banks, Stockbrokers, Savings   and Loan Associations and Credit Unions) WITH MEMBERSHIP IN AN APPROVED   SIGNATURE GUARANTEE MEDALLION PROGRAM, PURSUANT TO S.E.C. RULE 17Ad-15. The   following abbreviations, when used in the inscription on the face of this   certificate, shall be construed as though they were written out in full   according to applicable laws or regulations: TEN COM - as tenants in common UNIF   GIFT MIN ACT - ............................................Custodian   ................................................ TEN ENT - as tenants by the   entireties under Uniform Gifts to Minors   Act......................................................... JT TEN - as   joint tenants with right of survivorship UNIF TRF MIN ACT -   ............................................Custodian (until age   ................................) .............................under Uniform   Transfers to Minors Act ................... Additional abbreviations may also   be used though not in the above list.