He was made commander on 25 March 1796 and later that year put in command of the sloop HMS Zebra, and later the 16-gun HMS Savage. Savage was part of Sir Home Popham's squadron at Ostend, in May 1798. Thompson was made post captain on 11 August 1800, commanding in turn the 74-gun HMS Minotaur and then the 38-gun frigate HMS Perlen, in which ship he assisted at the reduction of Flushing in 1809 during the Walcheren Campaign.[1] He is also recorded as captain of HMS Foudroyant in 1807, part of the blockade off the coast of Portugal just before the Peninsular War.[2]