His first command was the brig HMS Swinger in 1808 as lieutenant-commander, with which he fought at the capture of the island of Deseada.

This was followed on 13 November 1808 by command of the brig Unique, from which (on 21 May 1809) he made a landing at Basseterre on Guadeloupe, spiking an enemy battery's guns despite being opposed by a large French regular force – he was the only unwounded man to return from the raid.

His next command came on 11 February 1812, with the 20-gun HMS Fawn in the West Indies, with which he fought against privateers until November 1814 and the end of the Napoleonic Wars.

His actions in that command gained him the cross[clarification needed] of the Légion d'honneur, the Order of St Anne 2nd class, the cross of the Order of the Redeemer, a British knighthood, a presentation sword from William, Duke of Clarence, Lord High Admiral, and a DCL from the University of Oxford.

Along with Sir William Abdy, 7th Baronet, Fellowes co-owned three sugar plantations in Antigua and St Vincent.