Stein, 33, served one season as UTSA's co-offensive coordinator and quarterbacks coach after two seasons as the Roadrunners' passing game coordinator and wide receivers coach. The Roadrunners rank ninth in FBS in total offense.
UTSA won its second straight C-USA championship on Friday behind a dominant offensive performance from quarterback Frank Harris, who went 32 of 37 for 341 yards, with four passing touchdowns and another rushing TD. Receiver Zakhari Franklin had 10 catches for 144 yards and three touchdowns, giving him 14 TDs on the season, third-most in the FBS. Under Stein, Harris has been one of the most productive quarterbacks in the country as UTSA finished 12-2 last season and 11-2 this year.
The Roadrunners have promoted tight ends/special teams coach Justin Burke to co-offensive coordinator to replace Stein.
Stein, who worked with current UTSA coach Jeff Traylor when they were both assistants under Charlie Strong at Texas, came to UTSA from Lake Travis High School in Austin, where he was offensive coordinator in 2018-19 and coached Longhorns quarterback Hudson Card, who has entered the transfer portal.
Stein played quarterback at Louisville from 2008-12.
On3 was first to report news of the move.