In 2004, Flynn was a third string quarterback as a redshirt freshman, behind starter Marcus Randall and backup JaMarcus Russell. He was also LSU's holder on placekicks. Flynn played in all 12 games, but only three games at quarterback. His collegiate first complete throw went to Xavier Carter for a 67-yard touchdown against Mississippi State. Flynn also made a short appearance in the 2004 Capital One Bowl. In that game, he completed 1 of 4 passes for 11 yards in a 25-30 loss against Iowa. He finished the year by completing 4 of 10 passes for 99 yards and 1 TD.