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.

[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.

[10] New University of Arizona head coach Brent Brennan hired Babers as offensive coordinator in February 2024.

[11] Brennan moved play-calling duties to tight ends coach Matt Adkins after week three of the season.