Brown moved on to Auburn University, where he majored in communications and played for coach Tommy Tuberville's Auburn Tigers football team from 2000 to 2004. He teamed up with speed running back Carnell Williams to create a premier running threat of speed and power. He redshirted after playing in the first two games of the 2000 season as he only gained 10 yards on six carries. In 2001, he played in 10 games and ranked third on the team with 330 yards on 84 carries and two touchdowns while catching seven passes for 109 yards.