Early senior career 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.
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. 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, 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.
Stevenage 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. On 30 April 2016, in the penultimate match of the season, Hughes scored his first goal for the club with a 78th-minute winner over
Wycombe Wanderers that saw Accrington remain in second place, two points clear of fourth place. The season ultimately ended poorly for Accrington as, despite hitting the woodwork three times, they were held to a 0–0 draw by
Stevenage on the final day of the season, with a 92nd-minute winner from
Bristol Rovers' defender
Lee Brown seeing Rovers sneak above Accrington into the third and final automatic promotion place, consigning Accrington to the play-offs. Hughes featured in both of the play-off semi final matches as Accrington lost 3–2 on aggregate to
AFC Wimbledon. Hughes was a part of the Accrington side that won the
2017–18 League Two title, featuring in all 46 league matches. Promotion to the third tier for the first time in the club's history was confirmed on 17 April 2018 when a double from
Billy Kee saw Accrington defeat
Yeovil Town. The title was confirmed on the penultimate day of the season with a 1–0 victory over
Lincoln City. Hughes was rewarded for his efforts over the season with a place in the
PFA League Two Team of the Year, along with two of his teammates,
Sean McConville and
Billy Kee. At the end of the season the club exercised a contractual option to retain him. In July 2019, Hughes signed a new one-year contract extension with the club having the option for a second year to keep him until the end of the
2020–21 season. On 27 March 2021, Hughes was forced off through injury in the 31' minute of what turned out to be his final appearance in an Accrington shirt, a 7–0 defeat to
Peterborough United. Until this injury, Hughes had played every minute of the season. Hughes was offered a new contract with the club at the end of the 2020–21 season.
Bristol Rovers On 26 May 2021, Hughes signed a one-year deal with League Two side
Bristol Rovers, the side that had narrowly beaten Accrington to promotion five years previously. He opted against signing the contract extension. Hughes made his debut for the club on the opening day of the
2021–22 season, giving away a 96th-minute penalty for a foul on
Oliver Hawkins that was converted by
Danny Johnson to give
Mansfield Town a 2–1 victory. Hughes picked up an Achilles injury in September 2021 in training that saw him out of action for the remainder of his time with the club, taking up a coaching role at times. ==Coaching career==