In 1813, Thompson transferred from HMS Bombay to take over as captain of HMS Aboukir whilst the latter ship was still on station in the Mediterranean. Aboukir remained on station in the Mediterranean, taking part in the capture of Genoa in April 1814 before returning to Chatham after Napoleon's defeat later that year and being decommissioned by 1816. He was in command of HMS Revenge c.1827, on the home station.[3] He was promoted to the rank of rear-admiral in 1830, and to that of vice-admiral in 1841.