Flynn redshirted the 2003 season at LSU. In 2004, he served as third-string quarterback behind starter Marcus Randall and backup JaMarcus Russell. He also doubled as LSU's holder on placekicks. Flynn played in all 12 games, but only three games as quarterback. His collegiate first completion went to Xavier Carter for a 67-yard touchdown against Mississippi State. Flynn also made a short appearance in the 2004 Capital One Bowl, completing 1 of 4 passes for 11 yards in a 25–30 losing effort against Iowa. He finished the season with 4 completions on 10 attempts for 99 yards and 1 touchdown.