Bowden attended and played football for West Virginia University, where he was a member of Phi Kappa Psi fraternity, and graduated magna cum laude with a degree in accounting.

In 1997, Auburn reached the SEC Championship Game, where they held as much as a 20–7 lead, but lost, giving up a fourth quarter 73-yard touchdown pass by Peyton Manning of the Tennessee Volunteers.

After starting with a 1–5 record, Bowden resigned as head coach the night before Auburn played against Louisiana Tech.

[5] In conversations with athletic director David Housel, Bowden was given no assurances he would have a chance to remedy the situation for the next season, and that he believed his termination was imminent.

[8] He also co-hosted "The Coaches Show" on Sirius Satellite Radio with Jack Arute and worked several times a month as a motivational speaker.

"[2] However, West Virginia offered the job to one of Rodriguez's assistants, Bill Stewart, who was the interim head coach when the Mountaineers upset the Oklahoma Sooners in the 2008 Fiesta Bowl.

At the end of the year, Bowden took the head coach position at a Division II school, North Alabama.

[11] Bowden was tapped to replace Mark Hudspeth, who left after directing the Lions to a 66–21 record and a third berth in seven years in the national playoff semifinals to become the passing game coordinator at Mississippi State University under new head coach Dan Mullen.

The Zips lost, 28–24, after an incomplete pass from the Wolverines' three-yard line on the final play of the game went out of the back of the end zone.

[13] Bowden's 2013 team showed improvement, compiling a 5–7 record on the season[14] and snapping the nation's longest road losing streak (28) with a 24–17 victory against the Miami RedHawks.

[19] In June 2019, Bowden joined the Clemson Tigers staff as an unpaid intern in addition to attending the university to receive a graduate degree.