Born in Liverpool, he joined Everton at the age of seven and progressed to the rank of reserve team captain. During his time at Everton, he spent a period in 2006 out on loan at Stockport County in League Two. He signed a new 1-year deal with Everton in April 2006 to keep him at the club until the summer of 2007. He was a regular captain for the reserves team and made three appearances in the Everton first team. He started in the Football League Cup game against Peterborough United on 20 September 2006 which Everton won 2–1, and came on as a substitute at half time against Luton Town in the following League Cup match which Everton won 4–0, as well as making his Premier League debut on 3 December 2006, being substituted on in the final minutes of a 2–0 victory over West Ham United at Goodison Park. He moved to Northampton Town on 31 January 2007 for an undisclosed fee and signed a two-year contract. He became a first choice centreback under Stuart Gray, and scored his first goal for the club against Rotherham United on 24 March. In June 2009 he did not take up an offer of a new contract with Northampton Town. On 8 July, Hughes signed for League One club Walsall on a free transfer. He scored his first goal for the club in a 3–2 win at Wycombe Wanderers on 31 October 2009. He was offered a new contract by Walsall on 10 May 2010.
North Queensland Fury
In June 2010, Hughes signed a contract with North Queensland Fury in the Australian A-League. The move came as a surprise, after signing contract acceptance forms with Walsall just one month earlier. He was given a role in the leadership group at the Fury upon arrival. Hughes quickly made a name for himself in the A-League, having to turn down contracts offered by several other A-League clubs midway through the season, including Sydney FC. In total, he scored four goals for the season including one penalty. He went on to be named the Fury's best player of the season at the club's awards night, in addition to receiving the People's Choice Award and the Player's Player Award. Hughes returned to England after North Queensland Fury ceased operations, and joined newly promoted League One club Bury F.C., having to turn down an offer from A-League club Newcastle Jets.
Bury
Hughes signed a two-year contract with Bury on 21 June 2011, subject to a medical and international clearing. This made him new manager Richie Barker's first signing for the club. Hughes scored his first goal for Bury in the opening game of his second season at the club on 12 August 2012, where Bury suffered a 2–1 defeat to Middlesbrough in the League Cup. Despite being a regular starter for Bury in the 2012–13 season, Hughes was loaned out to League Two side Accrington Stanley on 31 January 2013 for the remainder of the season. He made just five appearances for Accrington before returning to Bury early, after suffering a calf injury. Hughes was released by Bury at the end of the 2012–13 season, along with fifteen other players, following the club's relegation to League Two. He made a total of 60 appearances for Bury in his two seasons at the club.
Morecambe
Following his release from Bury, Hughes signed a two-year deal with League Two club Morecambe on 9 July 2013, and was named as the new club captain on arrival. He was then released by Morecambe on 7 May 2015.
Following the release from Morecambe, Mark Hughes signed for Stevenage on 27 May 2015. He was Teddy Sheringham's first summer signing. Hughes' first goal for the club was a late equaliser in a 2–2 draw with Newport County on 15 August 2015.
Accrington Stanley
Accrington exercised a contractual option at the end of the 2017–18 season to retain him.
