Allen played seven seasons for the Eagles, three seasons for the New Orleans Saints, and four seasons for the Oakland Raiders. While with the Eagles he was a very popular player with the "Gang Green" Defense, playing with NFL greats Reggie White, Seth Joyner, and Wes Hopkins. He is the only NFL player to run back three or more interceptions for scores in two separate seasons.
One of Allen's most memorable plays occurred October 3, 1993, in a game against the New York Jets. Having lost their starting quarterback (Randall Cunningham) to a fractured fibula early in the contest, the Eagles found themselves trailing the Jets by two points late in the 4th quarter as the Jets drove downfield for what would likely be the game's final points. Jets quarterback, Boomer Esiason, attempted to throw for a first down inside the Eagles 10-yard line as Allen stepped in front of the intended receiver at the 6-yard line. The ensuing 94-yard touchdown return was declared "Greatest Interception Return in NFL History" by Steve Sabol of NFL Films.
After several successful and injury-free seasons at Philadelphia and New Orleans, Allen blew out his knee during the 1998 season on November 15 while playing for the Oakland Raiders against the Seattle Seahawks and missed the rest of that season. But he came back strong in 2000 and had a season to remember, with six interceptions, including a team-record three for touchdowns. His teammates honored him with the first annual Eric Turner award for the Raiders' most outstanding defensive player. The award was created in the memory of the Oakland free safety who died of abdominal cancer in May 2000.
Through the 2001 season, Allen played in 214 of a possible 217 games.