Allen played college football for the Idaho State Bengals and was selected by the Kansas City Chiefs in the fourth round of the 2004 NFL draft.

After four years with the Chiefs, Allen was traded to the Minnesota Vikings in exchange for three draft picks, including a first-rounder.

Allen was born in Dallas, Texas, and raised on a horse ranch in Morgan Hill, California.

In 2001 Allen earned First-team All-Big Sky honors, and led the Bengals with 16 tackles for loss and 6.5 sacks.

In 2003, as a senior, Allen won the Buck Buchanan Award, recording 17.5 sacks, 102 tackles, 28 tackles for loss, six forced fumbles, three recovered fumbles, and nine pass deflections during 2003, ranking among the Big Sky Conference leaders in several defensive categories.

[9] Allen was selected by the Kansas City Chiefs in the fourth round (126th overall) of the 2004 NFL draft, and made the league minimum salary his first three years.

On May 21, 2007, Allen, as a restricted free agent, signed the Chiefs' one-year tender offer of US$2.35 million for the 2007 season.

[13] After leading the NFL in sacks in 2007 with 15.5, Allen was selected as a starting defensive end for the AFC in the 2007 Pro Bowl and was also named in the All-Pro team for 2007.

Allen also forced a safety when he chased Dan Orlovsky out of the end zone during a game against the Detroit Lions,[18] and he forced another safety in the week 10 game against the Green Bay Packers, when he sacked Aaron Rodgers in the end zone.

[19] On October 5, 2009, against the Green Bay Packers, Allen set a career-high with 4.5 sacks, as well as having his third safety in the previous two years.

In the season finale against the Detroit Lions, Allen scored his second career defensive touchdown, a 36-yard interception return.

[23] Allen fell seven votes short of winning AP NFL Defensive Player of the Year.

[24] On October 2, 2012, Allen was fined $7,875 for grabbing Tampa Bay Buccaneers lineman Donald Penn's facemask.

[26] Allen missed the week three game against the Green Bay Packers due to suffering from pneumonia and having lost 18 pounds.

[29] On September 28, 2015, Allen was traded to the Carolina Panthers for a conditional sixth-round pick in the 2016 NFL draft.

[31] During a Monday Night Football victory over the Indianapolis Colts, Allen had his first sack as a member of the Panthers on quarterback Andrew Luck to go along with five total tackles.

[33] On February 18, 2016, Allen announced his retirement by posting a video to his Twitter account of him riding his horse "into the sunset.

[40] He was inducted into the Pro Football Hall of Fame at the 14th Annual NFL Honors ceremony on February 6, 2025.

[43] In March 2018 he recruited fellow retired NFL players Marc Bulger, Keith Bulluck, and Michael Roos to form a competitive curling team.

[52] Allen was among four NFL players who were sent overseas on an NFL-USO tour to visit with U.S. military troops: "It has been one of the best experiences of my life – something that I'll never forget.

[53] In September 2010, Allen contributed $3,000 to Downey, California, animal shelter SEACCA's reward fund for information leading to an arrest, in connection to a horse being starved and abandoned on a Los Angeles city street.