The departure of Randall left Russell and Flynn battling for the starting quarterback position in the 2005 season. Russell eventually got the job, leaving Flynn as backup. He played in seven games at quarterback for the Tigers in 2005, completing 27 of 48 passes for 457 yards, 7 touchdowns and 1 interception. In a win over North Texas, Flynn threw a perfect 7-of-7 for 139 yards and 3 touchdowns, all in the fourth quarter. In the 2005 SEC Championship Game against the Georgia Bulldogs, starting quarterback Russell was injured and Flynn finished the game. He was then given the nod to start 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 rout of Miami.