Sir John Thynne (21 September 1555 – 21 November 1604) of Longleat House, Wiltshire, was an English landowner and Member of Parliament.
He was the eldest son of Sir John Thynne of Longleat and Christian, the daughter of Sir Richard Gresham, a London mercer and educated at Oxford University, graduating BA in 1573. He succeeded his father in 1580, inheriting Longleat House, which his father had built, and was knighted in 1603.
He served as a Justice of the Peace in Wiltshire, Gloucestershire, Hampshire and Shropshire and was appointed High Sheriff of Wiltshire for 1593–94.
He was elected a Member (MP) of the Parliament of England for Heytesbury in 1584, 1586, 1593, 1597 and 1601, and for Wiltshire in 1589 and 1604.
He married Joan, the daughter of Sir Rowland Heyward, Lord Mayor of London, of Cripplegate, London, with whom he had two sons. He was succeeded by his eldest son Thomas.