Perry started his career with Wimbledon, the team he supported as a boy, and grew up within walking distance of the club's ground at Plough Lane. He debuted in the early 1990s and went on to make over 200 appearances for the club. Such was his form, he was tipped by Manchester United manager Alex Ferguson and Crazy Gang bossJoe Kinnear to play for England. Perry moved from South to North London in July 1999, joining Tottenham Hotspur for a fee of £4 million, becoming the club's record signing. When teammate Sol Campbell moved to Arsenal, Perry became a first choice member of the team from the 2001–02 season, until he lost his place in the team in January 2003, after incurring a slipped disk. Three months later and upon his return he found himself amongst emerging youth players Ledley King and Anthony Gardner, and joined Charlton Athleticon loan in September 2003. Having impressed, his move was made permanent by Alan Curbishley in November 2003, after a £100,000 fee was agreed. Charlton were sitting in fourth place in the league at the time. He subsequently featured frequently in the league in the following two seasons and became an important part of the squad. When Iain Dowie replaced Curbishley as manager in May 2006, Perry was released from the club. He moved to West Bromwich Albion in July 2006, and made his debut a month later in a 2–0 win over Hull City. He helped the club reach the play-off final in the 2006–07 season. Perry criticised Derby County, who beat Albion in the final, predicting "they will come straight back down" from the Premier League. After being released by West Brom, having failed to make an agreed number of appearances to earn a new contract, Perry joined League One team Luton Town in July 2007. Perry scored his first goal for Luton in a 2–1 home win over Nottingham Forest on 27 October 2007. His performance in the match earned him a place in the League One Team of the Week. On 27 March 2008 he joined Southampton on loan for the rest of the season as a replacement for Andrew Davies, who broke his cheekbone and was ruled out for the remainder of the season. He was expected to go straight into the squad and make his debut against Cardiff City on 29 March. His performance in the 2–0 home win against Bristol City on 5 April 2008 saw him named in the Championship Team of the Week. On 6 June 2008 he joined Southampton on a free transfer. He scored his first goal for the club in the 2–1 home defeat to Birmingham City in August 2008. On 15 May2010, Perry was named in a list of 13 players to be released from Southampton before the start of the 2010–11 season.