In 2005, Hester played in 13 games with one start. He ran for 70 yards on 13 carries in a win against Miami in the Peach Bowl. Hester eventually finished the season with 114 yards and two TDs on 25 carries, and was also second amongst LSU running backs with 11 catches for 63 yards. He also participated in special teams, recording 14 tackles.
As a junior in 2006, he started at both tailback and fullback. Hester caught 35 passes for 269 yards, and ran for 440 yards, while also notching seven tackles on special teams.
As a senior in 2007, he was named a permanent team captain. He was the starting tailback for the Tigers. He rushed 225 times for 1103 yards and 12 touchdowns. He also had 14 catches for 106 yards and a touchdown. He was LSU's leading rusher in ten of fourteen games. His first 100 yard game came against Florida. Hester gained 106 yards and scored the game-winning touchdown. He was recognized as SEC Offensive Player of the Week and the Sporting News National Player of the Week for his efforts. Hester's longest run of the season came on an 87-yard touchdown against Louisiana Tech. He rushed for a career-high 126 yards on 28 carries against Arkansas. In the final game of his college career in the national championship game against Ohio State he rushed 21 times for 86 yards and a touchdown. He did all of this while being a part of a five-man rotation with Keiland Williams, Trindon Holliday, Charles Scott, and Richard Murphy.
In his preseason debut with the Chargers, Hester rushed for 49 yards over 13 carries, and scored two touchdowns against the Dallas Cowboys. In the Chargers' disappointingly low-scoring preseason game against the St. Louis Rams, Hester carried for 59 yards in 12 carries, but scored no touchdowns with an offensive line made up of mostly second- and third-string players.