Johann Ernst Graf von Thun und Hohenstein (3 July 1643 – 20 April 1709) was Bishop of Seckau from 1679 to 1687 and Prince-archbishop of Salzburg from 1687 until his death.

Born in Prague, Bohemia, he was a member of the Tyrolean Thun und Hohenstein noble family, elevated to the rank of Imperial Counts (Reichsgrafen) in 1629.

He was elected Bishop of Seckau in Styria on 29 December 1679 and consecrated by the Salzburg archbishop Max Gandolf von Kuenburg the next year.

The archbishop is best remembered as patron of the architect Johann Bernhard Fischer von Erlach, a leading proponent of Austrian Baroque church architecture.

Thun, backed by Pope Innocent XII, prevailed in lengthy quarrels with the Salzburg cathedral chapter as well as with the neighbouring Bishops of Chiemsee and Passau.