Johann Ernst von Thun und Hohenstein (July 3, 1643, Graz, Austria – April 20, 1709, Salzburg, Austria) was prince-archbishop of Salzburg, Austria, from 1687 to 1709. He was a member of the Thun und Hohenstein noble family.
He was originally from Tyrol and displayed a marked antipathy to the Italian designers and tastemakers that were emulated by many Austrians at the time. Upon his accession, he halted work on a church being built for an Italian order of monks and denied payment to Italian craftsmen.
On 21 Dec 1753 he ordained Siegmund Christoph von Schrattenbach bishop. and on 1 Jun 1749 Andreas Jakob von Dietrichstein. The archbishop is best remembered as patron of the architect Johann Bernhard Fischer von Erlach, a leader of Austrian Baroque church architecture. In 1697, the archbishop obliged all graduates of Salzburg's university to swear belief in the Immaculate Conception. Upon his death, Archbishop von Thun had his brain deposited in the university chapel, his entrails (symbolizing compassion) deposited in his Hospital Church, and his heart interred at his favorite Church of the Trinity.