Stoops, who spent the past two seasons as a defensive analyst at Alabama, will replace Jim Leavitt, who left to become defensive coordinator at SMU. Stoops, 59, last held a coordinator post at Oklahoma from 2012 to 2018, his second coordinator stint at OU under his brother, Bob.
"Mike brings tremendous experience to the defensive side of the ball," FAU coach Willie Taggart said in a statement. "His pedigree, two national championships, countless players to the NFL and his wealth of knowledge speaks for itself. This is a home run for us. As a former head coach and defensive coordinator at 'Power 5' programs, he knows the importance of building a defensive staff that can teach and adjust."
Stoops coached Arizona from 2004 to 2011, going 41-50 with three bowl appearances. He first served in a coordinator role at Oklahoma from 1999 to 2003, helping the Sooners to a national title in 2000. Stoops also spent three seasons in a coordinator role at Kansas State.
FAU went 5-4 in Taggart's first season and ranked 10th nationally in points allowed and 24th in total defense.