After four years at Villanova University Allen went undrafted in the 2000 NBA Draft. He began his career in the ABA with the San Diego Wildfire and in the International Basketball League with Trenton in 2000–01 season. On July 20, 2001 he was signed by the Miami Heat of the NBA. He stayed with the Heat until he was traded on February 24, 2005 to the Charlotte Bobcats. The Chicago Bulls signed him to a two-year deal on September 2, 2005. Over two seasons with the Bulls Allen played in 114 regular season games making 21 starts and averaged 4.5 points and 2.3 rebounds per game. On September 10, 2007 the New Jersey Nets signed Allen to a one-year contract worth US$964,636.
Allen appeared in 21 NBA Playoff games. He started all six playoff games for Chicago during '06 playoffs.