Thomas Wyndham (1508–1554) was an English naval officer and navigator.
The son of Sir Thomas Wyndham of Felbrigg (d. 1522) and Elizabeth Wentworth, he was educated at Louvain University and possibly in Italy. He held the office of Master of Ordnance of the Ships.
During the Anglo-Scottish war of the Rough Wooing, Wyndham commanded a ship at the landing at Edinburgh in 1544. In December 1547 he sailed two ships to Dundee to support the English garrison at Broughty Castle commanded by Andrew Dudley. He investigated the River Tay towards Perth looking to rob church roofs to make lead bullets. On Christmas Day 1547 he burnt Balmerino Abbey and on 29 December he burnt Elcho nunnery. On land, he constructed a battery at Haddington called 'Wyndham's bulwark.' With James Wilford on 3 June 1548, he captured Dalkeith Palace, and James Douglas, the future Regent Morton, and burnt the town, .
However, near the end of the war, the English commander, the Duke of Rutland, was required to investigate Wyndham's activities capturing foreign merchant vessels in the Firth. These disputed prizes included a coal-ship, seven Norwegian vessels laden with meal, pitch and timber, 4 French ships, a small warship he gave to Luttrell, another ship laden with soap and madder, and others. On the day peace was declared in England, 29 March 1550, Wyndham was sent to Scotland with two post horses and five Scottish hostages to exchange for his nephew John Luttrell who had been captured at Broughty.
Around 1550, Hans Eworth painted Wyndham's, Wilford's, and John Luttrell's portraits. Wyndham wears a powder flask at his neck and a gun over his shoulder inscribed, "TW, aetatis XLII.MDL," indicating he was 42 in 1550. In 1590, the picture was called, "Of Mr Thomas Wyndham drowned in the Sea returninge from Ginny."