Bowden attended North Mesquite High School in Mesquite, Texas, where he received All-American recognition. He received a scholarship from the University of Oklahoma. He didn't play in his first year because of failing to meet the requirements of Proposition 48.
In 1990, he led the team in tackles with 116 (3 for loss), while posting one interception, 4 passes defensed, one forced fumble and one fumble recovery. He gained All-American honors as a senior, while registering 75 unassisted tackles and 2 interceptions (both returned for touchdowns).
Bowden was selected in the fifth round (133rd overall) of the 1992 NFL draft by the Houston Oilers. From 1995 to 1997 he was a starter at outside linebacker. After being named the starter at middle linebacker in 1998, he was moved back to the outside during the Super Bowl XXXIV run in 1999, while registering 81 tackles, 3.5 sacks, 3 forced fumbles, 3 fumble recoveries and one interception.
Following the signing of Randall Godfrey in free agency and the drafting of Keith Bullock, Bowden became expendable and was not re-signed. He left after starting 84 of 123 regular-season games, while missing only 5 games and registering 521 tackles.
In 2000, the Dallas Cowboys had a lot of turnover at the linebacker position and the signing of Bowden in free agency was one of the moves made to improve the depth. He was the backup to Darren Hambrick and played in all 16 games. He was cut on April 20, 2001, after failing a physical.
From 2008 to 2011, Bowden held coaching positions at Oklahoma City high schools, Mount St. Mary High School and Edmond Santa Fe High School.
In 2006, Bowden was hired as the secondary coach for the Central Oklahoma Bronchos. He held this position for 3 seasons through the year of 2008.
In 2012, Bowden was hired by the St. Louis Rams to become an assistant linebackers coach. On March 1, 2016, he was moved to assistant special teams coach, before leaving the team on March 17, 2016 for a job at a higher position.
On March 17, 2016, Bowden was hired by the San Francisco 49ers. He was appointed to the position of inside linebackers coach after Hardy Nickerson (who was hired in January 2016) abruptly quit and took a job as the Illinois defensive coordinator for his former coaching companion Lovie Smith who was also just hired by the Illini.
NFL head coaches under whom Joe Bowden has served:Jeff Fisher, St. Louis Rams (2012-2015)
Chip Kelly, San Francisco 49ers (2016–present)
Bowden is currently an inside linebackers coach for the San Francisco 49ers of the NFL. In 1998, he married Malika (Welch) and they have two daughters, Sydney and Cheyenne. He has one son, Jaylon who also plays football and is following in the footsteps of his father.