Born in Scotland, Hughes grew up in Italy and began his career as a youth player at Serie A side Atalanta. After moving back to the UK, Hughes spent five years with Arsenal as a youth player. He did not make the transition to the first team and so left the club to join Bournemouth in the summer of 1998.
Bournemouth
Hughes made his debut for Bournemouth in a 2–0 victory over Lincoln City, and became a regular member of the first team. He was signed by Portsmouth for £50,000 in summer 2002.
Portsmouth
After making his debut for Portsmouth in a 1–1 draw at Sheffield United, Hughes was loaned out to Grimsby Town, where he played 12 games and scored one goal against Brighton. He was given a Premier League appearance in December 2003, and he remained a squad member for the remainder of the 2003–04 campaign. He scored the winning goal, his first for Portsmouth, in a 1–0 FA Cup victory over Liverpool on 22 February 2004. On 28 July 2006 he pledged his future to the club, signing a three-year contract. On 15 August 2007, playing against Manchester United, Hughes was headbutted by Cristiano Ronaldo, after Hughes allegedly provoked him. Ronaldo was red-carded for his actions. The game finished 1–1. Hughes was part of Portsmouth's 2007–08 FA Cup-winning team. Despite not making the squad for the final he appeared in the earlier rounds. In January 2009, Hughes was offered an extension to his Portsmouth contract. His second competitive goal for Portsmouth came when he scored in a 4–1 League Cup win against Hereford on 25 August 2009. Hughes' first league goal for Portsmouth came in a 3–3 draw against Leeds United at Elland Road on 28 December 2010, his last game for the club. The Scottish midfielder's strike deflected off Leeds defender Andy O'Brien on its way into the net. Originally awarded as an own goal to O'Brien, the goal was subsequently credited to Hughes by the dubious goals committee as his first league goal for the club. Hughes played his last game for Portsmouth on 28 December 2010. Under the terms of his contract, signed when Portsmouth were still in the Premier League, he was entitled to a new contract with increased wages if he had played one more game. As Portsmouth could not afford to fulfil the original offer, and he was not prepared to accept alternative terms; he remained at Portsmouth without playing in the second half of the 2010–11 season. He was subsequently released at the end of the season.
Return to Bournemouth
In the summer of 2012, a year after retiring from the game, Hughes was convinced to come out of retirement by Paul Groves, who managed him at Grimsby and was assistant manager while Hughes was at Portsmouth. In turn he re-joined Bournemouth following Groves' appointment as manager. Hughes made his second debut for Bournemouth in a 5–3 loss at Sheffield United on 1 September 2012, coming on as a 46th-minute substitute for Shaun MacDonald. On 8 September, Hughes scored the only goal in the match against Yeovil, securing Bournemouth their first League One victory. In May 2014, with his contract due to expire, Hughes took the decision to retire aged 34. Hughes revealed he planned on life after retirement, working for BT Sport as a pundit and running a restaurant with his brother. He later joined Bournemouth's recruitment team under Eddie Howe.
