Thomas Stoughton (25 March 1521–1576), of Stoughton, Surrey and West Stoke, Sussex, was an English politician.
The Stoughton family had long sat in Parliament for this area. Stoughton was the son of Lawrence Stoughton of Stoughton and Anne nee Combes of Guildford. Stoughton married twice, first to Anne Fleming from London, no recorded children. His second wife, who he married on 27 February 1553, was Elizabeth Lewknor of Tangmere, Sussex. They had two sons, both MPs: Adrian (for Haslemere and Chichester) and Lawrence (who represented Guildford), as well as two daughters.
Stoughton was a Member of Parliament for Chichester in March 1553, October 1553, April 1554 and 1563. He represented Guildford in 1547, 1559 and 1572.