Amendment: SEC Form SC 13D/A filed by BeiGene Ltd.

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

SCHEDULE 13D

(Rule 13d-102)

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. 11)*

BeiGene, Ltd.

(Name of Issuer)

Ordinary Shares, par value $0.0001 per share

(Title of Class of Securities)

07725L102**

(CUSIP number)

Alexandra A. Toohey

Chief Financial Officer

Baker Bros. Advisors LP

860 Washington Street, 3^rd Floor

New York, NY 10014

(212) 339-5690

(Name, address and telephone number of person authorized to receive notices and communications)

December 9, 2024

(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    ¨

(Continued on the following pages)

(Page 1 of 9 Pages)

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*The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

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 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

**This CUSIP applies to the American Depositary Shares, each representing thirteen Ordinary Shares

(1) Includes 123,914,440 of the Ordinary Shares (“Ordinary Shares”) of BeiGene, Ltd. (the “Issuer”) reported that are beneficially owned through American Depositary Shares (“ADS”), 93,392 Ordinary Shares received from vested restricted stock units of the Issuer and 813,072 Ordinary Shares underlying 813,072 options to purchase Ordinary Shares (“Share Options”). Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with Securities and Exchange Commission (“SEC”) on November 12, 2024.

(1) Includes 123,914,440 Ordinary Shares reported that are beneficially owned through ADS, 93,392 Ordinary Shares received from vested restricted stock units of the Issuer and 813,072 Ordinary Shares underlying 813,072 Share Options. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with SEC on November 12, 2024.

(1) Includes 123,914,440 Ordinary Shares reported that are beneficially owned through ADS, 93,392 Ordinary Shares received from vested restricted stock units of the Issuer and 813,072 Ordinary Shares underlying 813,072 Share Options. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with SEC on November 12, 2024.

(1) Includes 123,914,440 Ordinary Shares reported that are beneficially owned through ADS, 93,392 Ordinary Shares received from vested restricted stock units of the Issuer and 813,072 Ordinary Shares underlying 813,072 Share Options. Each ADS represents 13 Ordinary Shares of the Issuer.

(2)  Based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with SEC on November 12, 2024.

(1) Includes 144,508 Ordinary Shares reported that are beneficially owned through ADS.

(2) The percentage is less than 0.1% based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with SEC on November 12, 2024.

Amendment No. 11 to Schedule 13D

This Amendment No. 11 to Schedule 13D amends and supplements the previously filed Schedules 13D filed by Baker Bros. Advisors LP (the “Adviser”), Baker Bros. Advisors (GP), LLC (the “Adviser GP”), Julian C. Baker, Felix J. Baker and FBB3 LLC (“FBB3”) (collectively the “Reporting Persons”). Except as supplemented herein, such statements, as heretofore amended and supplemented, remain in full force and effect.

The Adviser GP is the sole general partner of the Adviser. Pursuant to the management agreements, as amended, among the Adviser, Baker Brothers Life Sciences, L.P. (“Life Sciences”) and 667, L.P. (“667”, and together with Life Sciences, the “Funds”), and their respective general partners, the Funds’ respective general partners relinquished to the Adviser all discretion and authority with respect to the investment and voting power over securities held by the Funds, and thus the Adviser has complete and unlimited discretion and authority with respect to the Funds’ investments and voting power over investments.

Item 5. Interest in Securities of the Issuer.

Item 5 of this Schedule 13D is hereby supplemented and amended, as the case may be, as follows:

(a) and (b) Items 7 through 11 and 13 of each of the cover pages of this Amendment No. 11 are incorporated herein by reference.

Set forth below is the aggregate number of Ordinary Shares of BeiGene, Ltd. (the “Issuer”) directly held by the Funds, 123,914,440 of which are directly held by the Funds through American Depositary Shares (“ADS”), along with the percentage of the Issuer’s outstanding Ordinary Shares such holdings represent. Each ADS represents 13 Ordinary Shares of the Issuer. The information set forth below is based on 1,386,034,320 Ordinary Shares outstanding at November 1, 2024 as reported in the Issuer’s Form 10-Q filed with Securities and Exchange Commission (“SEC”) on November 12, 2024. Such percentage figures are calculated in accordance with Rule 13d-3 under the Securities Exchange Act of 1934, as amended.

Michael Goller and Ranjeev Krishana, full-time employees of the Adviser, have served on the Board since April 21, 2015 and October 7, 2014, respectively. Michael Goller and Ranjeev Krishana currently serve on the Board as representatives of the Funds. Michael Goller and Ranjeev Krishana each hold 406,536 options to purchase Ordinary Shares (“Share Options”) received in connection with their service on the Board which are exercisable within 60 days from the date of this Amendment No. 11. Michael Goller and Ranjeev Krishana each hold 46,696 Ordinary Shares which were received upon the vesting of restricted stock units (each, an “RSU”) in connection with their service on the Board. Michael Goller and Ranjeev Krishana each hold 16,341 RSUs and 34,151 Share Options with an exercise price of $12.23 per Ordinary Share which were granted on June 5, 2024 in connection with their service on the Board and which vest on the earlier to occur of the first anniversary of the grant date or the date of the next annual general meeting of the Issuer. The policy of the Funds and the Adviser does not permit managing members of the Adviser GP or full-time employees of the Adviser to receive compensation for serving as directors of the Issuer, and the Funds are instead entitled to the pecuniary interest in any compensation received for their service.

The Adviser has voting and investment power over the RSUs, Share Options and Ordinary Shares underlying such Share Options and Ordinary Shares received from the exercise of Share Options by Michael Goller and Ranjeev Krishana as director’s compensation. The Adviser GP, and Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition of the Share Options, Ordinary Shares received from the exercise of Share Options and Ordinary Shares underlying such Share Options held by Michael Goller and Ranjeev Krishana as director’s compensation.

The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.

Julian C. Baker and Felix J. Baker are also the sole managers of FBB3 and by policy they do not transact in or vote the securities of the Issuer held by FBB3.

(c) The following transactions in ADS were effected by the Funds noted below during sixty days preceding the filing of this statement. All transactions were effected in the over-the-counter market or the open market directly with a broker-dealer. Except as disclosed herein or in any previous amendments to this Schedule 13D, none of the Reporting Persons or their affiliates has effected any other transactions in securities of the Issuer during the past 60 days.

(1) The reported price is a weighted average price. These shares were traded in multiple transactions at a prices ranging from $208.000 to $208.185. The Reporting Persons undertake to provide the staff of the Securities and Exchange Commission (the “Staff”), upon request, full information regarding the number of shares traded at each separate price within the ranges set forth in this footnote.

(d)  Certain securities of the Issuer are held directly by 667, a limited partnership the sole general partner of which is Baker Biotech Capital, L.P., a limited partnership the sole general partner of which is Baker Biotech Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Biotech Capital (GP), LLC.

Certain securities of the Issuer are held directly by Life Sciences, a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Brothers Life Sciences Capital (GP), LLC.

(e) Not applicable.

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.

December 10, 2024