Commodore Thomas Warren (died 12 November 1699) was a Royal Navy officer who became Commander-in-Chief, Portsmouth.

Promoted to captain on 28 May 1689, Warren was given command of the fifth-rate HMS Hopewell in 1690, the fifth-rate HMS Sweepstakes in 1691 and the fourth-rate HMS Crown in 1692.

[1][2] In December 1698, Warren was tasked with obtaining the surrender of pirates under the 1698 Act of Grace,[3] commanding a squadron consisting of HMS Anglesea, HMS Harwich, HMS Hastings and HMS Lizard.

By the time the squadron arrived at Madagascar's Île Sainte-Marie on 29 January 1699, the terms of the Act had expired; therefore, Warren promised to have the dates extended.

However, in the case of pirates such as the crew of William Kidd, it was ruled that Warren did not have the authority to make such an extension, thus invalidating the pardons.