Allen signed with the Chicago Bears on December 10, 1997, though he was released on August 26, 1998. He later was brought back on September 1, and placed on the Bears practice squad. Allen was the Bears starting halfback, and in 2000, he led the team with 1,120 rushing yards and two touchdowns. During the season, Allen became the first Bears player to run for 100 yards since the 1998 season when he ran for 163 yards in his first career start against the Baltimore Ravens. However, in a loss to the New York Jets, Allen fumbled three times. Allen's starting role was claimed by Anthony Thomas in 2001. Against the Cleveland Browns in Week 8, Allen caught the game-tying Hail Mary pass from Shane Matthews that was deflected towards Allen, as the Bears went on to defeat the Browns 27–21.
