Brown entered the 2009 season as the primary backup to Joseph Addai, and scored his first career touchdown in Week 2 against the Miami Dolphins. Brown missed Weeks 8 and 9 due to a strained left shoulder, and later missed three games with a chest injury. Brown returned to start the regular-season finale in place of Addai, who was resting for the playoffs. He finished the 2009 regular season with 281 rushing yards and three touchdowns.
Brown rushed 12 times for 28 yards in the Colts two playoff wins leading up to Super Bowl XLIV. Brown rushed four times for 18 yards in the Super Bowl loss to the Saints.