The new job will mark Petrino's first head coaching job after several years as an assistant coach, including three of the last five season as offensive coordinator for the Hogs.
Petrino is set to takeover an Idaho team that finished 1-11 this season and has won just 20 games since 2007.
The Vandals will be competing as an independent starting next season after the Western Athletic Conference gave up football following the 2012 season.
Petrino was born and raised in nearby Montana. He has been a college coach for more than 20 years, getting his start at Carroll College where his father coached for many years.