Bowen accepted a football scholarship from Hofstra University, where he was converted into a defensive end and became a three-year starter. As a freshman, he played in 5 games, making 3 tackles. As a sophomore, he appeared in 12 games, recording 49 tackles, 3 sacks and one fumble recovery. He had 8 tackles against the University of Rhode Island. As a junior, he started at right defensive end, registering 68 tackles, 7.5 tackles for loss and 3 sacks. He had 9 tackles against the University of New Hampshire. As a senior, he tallied 48 tackles, 5.5 sacks, one interception and 2 passes defensed. He finished his career with 168 tackles, 11.5 sacks and one interception, which was returned for a 31-yard touchdown.
Bowen was signed as an undrafted free agent by the Dallas Cowboys after the 2006 NFL Draft on May 1. He was released on September 2 and signed to the team's practice squad two days later. On November 8, he was promoted to the active roster. He appeared in the season-ending loss to the Detroit Lions and made his first career sack against Jon Kitna. In 2007, Bowen served as a back-up to starting right defensive end Chris Canty, recording 9 quarterback pressures and 23 tackles. In 2008, he played in 14 games, posting 28 tackles, 9 quarterback pressures. In 2009, he appeared in all 16 games as the backup to Igor Olshansky and registered a then career-high 31 tackles, 3 sacks and 33 quarterback pressures. In 2010, he appeared in all 16 games, starting 9 contests in place of an injured Marcus Spears, while finishing with 25 tackles, 12 quarterback pressures, 1.5 sacks and one pass defensed.
Washington Redskins
2011 season
On July 28, the Washington Redskins signed Bowen to a five-year, $27.5 million contract. In his first season with the team, he was named the starting right defensive end in a 3–4 defense. On November 28, he was diagnosed with a third degree PCL tear, suffered against the Seattle Seahawks. He didn’t need surgery and managed to start in all 16 games for the first time in his career He set new career-highs with 41 tackles and six sacks. He received the team's Ed Block Courage Award not just for overcoming injury, but also for the passing of his son and his mother-in-law.
2012 season
Bowen had arthroscopic surgery on his left knee in mid-April, to fix complications from his previous year knee injury. On November 14, he was made a co-defensive captain after a team vote during the Redskins' bye week. In the Week 14 win against the Cleveland Browns, he tore his upper left biceps and would still play for the rest of the regular season. He would make an essential defensive move in the next week against the Philadelphia Eagles. During the Eagles last attempt to tie the game and with seconds remaining, Bowen put enough pressure on Nick Foles to make him throw the ball into the turf. Despite one second remaining on the clock, Foles would receive an intentional grounding penalty, ending the game and giving the Redskins the victory. He registered 51 tackles, 32 quarterback pressures, 3 passes defensed and one sack.
2013 season
In the Week 7 win against the Chicago Bears, Bowen suffered a tear in his right PCL. He continued to play through the injury until he further injured his right knee in a Week 11 loss to the Philadelphia Eagles. On November 26, the Redskins moved him to injured reserve due to needing a microfracture surgery to repair his torn PCL. He finished the season with 19 tackles and one pass defensed.
Having spent all of training camp on the PUP list, it was confirmed that he would remain there at the start of the 2014 season. He was placed on the active roster on October 18. He appeared in just 8 games, while registering 11 tackles and no sacks. He was released on February 27, 2015,
On March 24, Bowen was signed as a free agent by the New York Jets, reuniting with Todd Bowles, who was a Dallas Cowboys assistant coach. He was a reserve player and appeared in 15 games with one start. He announced his retirement on June 1, 2016, signing a one-day contract with the Washington Redskins. He finished his professional career with 128 games, 175 tackles, 12.5 sacks and 9 passes defensed.
Bowen married his college girlfriend Tiffany Johnson, in March 2008. The couple have 3 children-one daughter, Trinity, and twin boys, Stephen III and Skyler. Bowen's twin sons were born four months prematurely on June 28, 2011, the same day he signed with the Redskins. Unfortunately, Skyler died 10 days later. On December 8, 2011, Bowen won the Redskins’ Ed Block Courage Award in recognition of the inspiring way he dealt with Skyler's death. He is best friends with former NFL defensive end Jason Hatcher. Both of them started their NFL careers with the Dallas Cowboys in 2006.
