OXFORD, Mississippi (AP) -- The school confirmed Freeze's resignation in a release Thursday night. Assistant Matt Luke has been named the interim coach.
The Rebels had a quick rise under Freeze, recruiting at a high level and reaching an apex with a Sugar Bowl victory over Oklahoma State following the 2015 season.
But an NCAA investigation into the program - alleging 21 charges of academic, booster, and recruiting misconduct - has overshadowed much of that success, especially over the past year. The school has already self-imposed several penalties, including a one-year postseason ban for the upcoming season.
Freeze - who was making more than $5 million per year - had a 39-25 record over five seasons, including a 19-21 mark in the Southeastern Conference.