After playing non-League football for Westfields, Bowyer, a full back, signed for Football League team Hereford United on non-contract terms, making 14 appearances in the 1989–90 season. After the season ended, Bowyer moved to Nottingham Forest, but he never made a senior Football League appearance for them. Bowyer later signed for Rotherham United, making 38 appearances in the League over the next two seasons, before retiring due to injury. Whilst at Rotherham he was a part of the team that won the 1996 Football League Trophy Final.
Coaching career
After retiring as a player, Bowyer began his coaching career working part-time at Ilkeston. before being appointed as Under-17 coach at Derby County, where he spent six years as an academy coach. He then became Under 18's coach for Blackburn Rovers in 2004. He became Reserve Team manager in 2008, and in December 2012 he was appointed as caretaker manager following the dismissal of Henning Berg, steering them to a 3–1 victory over Barnsley in his first game in charge. It was later announced that Bowyer would remain in charge until the end of January. Bowyer was re-appointed Caretaker Manager on 19 March 2013, following the sacking of Michael Appleton, until the end of the season. However, on 26 March 2013 Bowyer said he was unsure how long he would remain in the position, in case the club hired a new permanent manager, and on 8 April 2013 Bowyer was summoned to India for a meeting with the club's owners. Bowyer was appointed the permanent manager of Blackburn on 24 May 2013, on a 12-month rolling contract. In September 2015, he called for goal line technology to be implemented. On 10 November 2015 Bowyer was sacked as manager of Blackburn Rovers. On 1 June 2016, Bowyer was appointed as manager of Blackpool on a one-year rolling contract, following the club's relegation to EFL League Two. On 18 March 2017 he was hit by boiled sweets thrown by Newport County opposition fans. On 28 May, Bowyer guided Blackpool to an immediate return to EFL League One in his first season in charge, his side beat Exeter City 2–1 in the League Two play-off final. He resigned as Blackpool manager on 6 August 2018. In February 2019 he was linked with the vacant managerial position at Bradford City. On 4 March 2019 Bowyer replaced David Hopkin as Bradford City manager, signing a contract until the end of the season, with Andy Todd as his assistant. He said that all of City's squad players would have a chance to fight for a first-team place. Bowyer retained the club's other coaching staff, including Martin Drury who had been caretaker manager prior to his appointment. In April 2019 he signed a contract with Bradford City until 2021. He was nominated for the League TwoManager of the Month award for October 2019, but later said he was not a 'fan' of such awards. He was sacked on 3 February 2020.