On 1 July 2017, Bowyer was appointed as assistant manager of Charlton Athletic.
Bowyer played for youth team Senrab before joining Charlton Athletic as a schoolboy. He turned professional in April 1994. He first drew attention in 1995, when he and teammate Dean Chandler failed a drugs test for cannabis use. Bowyer was dropped from the England under-18 squad and suspended for eight weeks while he took part in a rehabilitation course organised by the Football Association (the FA). He went on to become a first-team regular, making 58 appearances for Charlton and scoring 14 goals.
In 1996, he was signed by Leeds United manager Howard Wilkinson for £2.8 million, which was a record for a British teenager. Later the same year, Bowyer was convicted of affray and fined £4,500 following an incident in a McDonald's restaurant in London in which CCTV footage showed Bowyer throwing chairs and racially abusing a staff member of Asian origin.
Initially, Bowyer was kept out of the Leeds first team by Alf-Inge Håland and David Hopkin; he eventually replaced Hopkin in the 1998–99 season, and from then on was a first-team regular. He was a key player in David O'Leary's Leeds side that qualified for the Champions League in 1999–2000, and which reached the semi finals of the UEFA Cup in 2000 and the Champions League in 2001. In the Champions League run he scored crucial goals against A.C. Milan, Barcelona and Anderlecht. He was voted the Leeds player of the year by supporters in both 1998–99 and 2000–01.
Following an incident near a Leeds nightclub in January 2000, in which an Asian student suffered severe injuries, Bowyer and teammate Jonathan Woodgate were charged with causing grievous bodily harm with intent and affray. An initial trial collapsed in April 2001 after an article in a Sunday newspaper, and following a second trial, which ended in December 2001, Bowyer was cleared of both charges while Woodgate was convicted of affray and sentenced to community service. Bowyer was generally recognised as playing some of the finest football of his career during this period and would often go straight from court to play for Leeds. In 2005, the player agreed a £170,000 out-of-court settlement of a civil action for damages brought by the victim and his brother, who had been less seriously hurt in the assault.
After Bowyer's acquittal, Leeds fined him four weeks' wages for a breach of the club's code of conduct. Despite having had the backing of the club during the trial and the club paying his extensive legal fees, Bowyer took exception to the fine and was placed on the transfer list. The dispute was later settled and Bowyer removed from the transfer list, though he returned to it at the end of the season after turning down a new five-year contract. A £9 million fee was agreed for a move to Liverpool, which fell through with manager Gérard Houllier not convinced the player had the "hunger or desire" to play for the club. In January 2003, Bowyer signed for West Ham United. He had made 265 appearances for Leeds in all competitions, scoring 55 goals.
Bowyer signed for West Ham United on an initial six-month contract for a nominal transfer fee, which meant that should West Ham be relegated at the end of the 2002–03 season, the club would not be burdened with a large Premiership salary. The transfer was not popular with a section of West Ham supporters who questioned Bowyer's attitude towards racism. A protest against his signing was held outside Upton Park before Bowyer's introduction to the crowd. Claims that Bowyer would have received a £1 million bonus had West Ham stayed up were denied by the club's then manager Glenn Roeder. In the event, Bowyer was hampered by ankle injuries and made only eleven appearances for West Ham. West Ham were relegated and Bowyer was not offered another contract.
After West Ham were relegated at the end of the 2002–03 season, Bowyer joined Newcastle United on a free transfer in July 2003.
In April 2005, Bowyer was in the media spotlight again after an on-pitch brawl with teammate Kieron Dyer in Newcastle United's Premiership match with Aston Villa. This resulted in a red card, plus an automatic three-game ban, for each player. The Football Association fined Bowyer £30,000 and imposed an additional three-game ban, and the club fined him six weeks' wages; Dyer was not fined as Bowyer was perceived to have thrown the first punch. In addition, Bowyer was charged by Northumbria Police in connection with the brawl with offences under section four of the Public Order Act. He pleaded guilty to the lesser charge of using threatening behaviour and was fined £600 and ordered to pay £1000 costs.
Bowyer made 98 appearances for Newcastle in all competitions and scored 11 goals.
Bowyer rejoined West Ham United, the club he supported as a boy, in June 2006 for an undisclosed fee, declaring that he had "unfinished business" with the club. He made 22 appearances in the 2006–07 season, which was disrupted by a dislocated shoulder suffered in West Ham United's 6–0 loss to Reading in January 2007. However, Bowyer made a quick and sooner-than-expected recovery and played in five of West Ham's crucial games towards the end of the season.
He regained a regular place in the Hammers first team at the beginning of the 2007–08 season, scoring his first goals for West Ham against Wigan Athletic and Middlesbrough, and then two more in the 5–0 victory over Derby County.
In January 2009, Bowyer signed for Birmingham City on loan until the end of the 2008–09 season. He made his debut on 17 January at home to Cardiff City in the Championship, scoring an equalising goal in the fourth minute of stoppage time to make the score 1–1. Following the expiry of his contract with West Ham United, Bowyer signed a two-year contract with Birmingham in July 2009. He scored winning goals in consecutive Premier League matches, against Fulham and Wolverhampton Wanderers, to take Birmingham into a mid-table position at the end of November, and was part of the team that went on a run of 15 games unbeaten in all competitions, including a club record 12 unbeaten in the top flight, as they finished in ninth place, the club's best for more than 50 years.
In September 2010 Bowyer was forced to apologise for verbally abusing a West Bromwich Albion supporter. The incident occurred following Bowyer's substitution after he had committed a rash challenge on Gabriel Tamaș. In the absence through injury of Craig Gardner, Bowyer returned to the starting eleven for the match against champions Chelsea in November 2010, scored the only goal of the game to give his team a surprise victory, and following up with a late equaliser against Manchester United. In January 2011, television replays highlighted incidents, unnoticed by the match referee, in which Bowyer stamped on Arsenal defender Bacary Sagna and appeared to rake his studs down the same player's Achilles. Suggestions in the media that Bowyer could receive a six-match ban prompted Birmingham manager Alex McLeish to argue that the football authorities were not treating all clubs equally when using television evidence. Bowyer received the standard three-match ban for violent conduct.
From 2010, Bowyer held the record for most yellow cards received in the Premier League; by the end of that year, he had 98 yellow cards in the competition as well as five red.
He made his first appearance in a major final in February 2011, in the starting eleven as Birmingham defeated favourites Arsenal 2–1 in the League Cup Final at Wembley Stadium. At that time, it was reported that he was not to be offered a contract extension, in May, McLeish indicated an offer would be made, but after Birmingham's relegation to the Championship, Bowyer left the club when his contract expired at the end of the 2010–11 season.
On 10 July 2011, Ipswich Town signed Bowyer as a free agent. He scored his first goal for Ipswich with a late winner against former club West Ham United on 27 September. He was released at the end of the 2011–12 season, having scored twice in 29 appearances.
During his early career at Leeds, Bowyer was a regular in the England under-21 team, making 13 appearances for the national side.
Bowyer's form during the 2000–01 season led to calls for inclusion in the England squad; however, the Football Association ruled that he could not be selected until the court case in relation to an assault on an Asian student was completed. The FA eventually cleared Bowyer for selection following the conclusion of the court case and England manager Sven-Göran Eriksson called him into the squad for an international friendly against Portugal in September 2002. Bowyer made his England debut in the game, setting up a goal for Leeds teammate Alan Smith. It was his only appearance for England.
Having fished all of his adult life, Bowyer had taken a week summer break every June with friends at a carp fishing lake in the French village of Orconte. After being released by Ipswich, he bought the 12 acres (4.9 ha) property. Renamed Étang de Bows (English: Bows' Lake), he spends his time between there and his family home in Essex, with his wife and two children. In autumn 2015 he spent a month as a guest coach of Watford's under-21 team, working under former Leeds teammate Harry Kewell.
After coaching at his first professional club, Charlton Athletic, Bowyer was appointed assistant manager under Karl Robinson on 1 July 2017.Birmingham City
Football League Cup: 2011