Babers began his coaching career as a graduate assistant at Hawaii in 1984. From there, Babers coached at numerous schools highlighted by offensive coordinator positions at both Arizona and Texas A&M as well as an assistant head coach position with UCLA. After four years as an assistant at Baylor, on December 9, 2011, Babers was named as the new head football coach at Eastern Illinois University to replace Bob Spoo.[4] In two seasons at Eastern Illinois, the Panthers made the playoffs both times,[3] led by quarterback Jimmy Garoppolo, who was a second-round pick in the 2014 NFL draft.
On December 5, 2015, Babers became the head coach at Syracuse.[7]
After a 10-win season in 2018, Babers received a contract extension through the 2023 season.[8][9] Babers was fired from his role as head coach at Syracuse on November 19, 2023, one game before the end of the 2023 regular season. Babers had only two winning seasons during his eight years at Syracuse.[10]