 At Kentucky, Bonner was the backup quarterback behind eventual #1 overall NFL draft pick Tim Couch during the 1998 season in which the Wildcats ended up in the Outback Bowl after winning seven games.Couch went to the NFL after his junior season and Bonner became the starting quarterback in 1999.In 1999, Bonner started all 12 games and led the Southeastern Conference in pass efficiency, total offense, and passing yards per game.