When Randall left the team, Russell and Flynn fought for the starting QB position. Russell got the job. Flynn was the backup. Flynn played in seven games at quarterback for the Tigers in 2005. He completed 27 of 48 passes for 457 yards, 7 touchdowns and 1 interception. In a win over North Texas, Flynn threw 7-of-7 for 139 yards and 3 TDs, all in the fourth quarter. In the 2005 SEC Championship Game against the Georgia Bulldogs, starting quarterback Russell was injured. Flynn finished the game. He was then made the main quarterback for the Tigers in the 2005 Chick-fil-A Peach Bowl against the University of Miami Hurricanes. In that game, he led the Tigers to a 40-3 win over Miami.