Milligan started his grassroots football career at his local club, Birrong Sports Football club in the Bankstown District in 1991 and 1992, and he quickly moved onto representative football as a junior footballer.
Early career FourFourTwo magazine revealed on 28 July 2007 that after the Asian Cup Milligan had gone without
Sydney FC's permission to trial for teams in Europe. Milligan was linked with French sides
Metz and
Lens. The following day Milligan reportedly walked out on Metz just before a scheduled trial game appearance against
Standard Liège, allegedly out of frustration at the right-back position he would be trialled in. The following day it was reported that Milligan would return home to play for Sydney FC after all. During the summer of 2008, he was linked with a move to English
Premier League clubs
Blackburn Rovers,
Manchester City and
Arsenal, Lens of
Ligue 1, as well as with
Porto in the
Primeira Liga and
Bundesliga side
Werder Bremen. On 21 October 2008,
The Sydney Morning Herald reported that Milligan had signed a guest contract with
Newcastle United Jets for seven weeks. He made his debut on 24 October 2008, against
Central Coast Mariners at
Bluetongue Stadium,
Gosford, where his team lost 1–0. During this time he was also sent off in a match against the
Wellington Phoenix.
Asia Milligan joined
Chinese Super League outfit
Shanghai Shenhua in January 2009, signing a three-year contract. On 19 May, Milligan scored his first goal for Shanghai Shenhua in their 1–1 draw in the
AFC Champions League group stage match against
Kashima Antlers. Milligan finalised his switch from Chinese side Shanghai Shenhua to Japanese side
JEF United Chiba, who were relegated to the second division. When the
2011 Tōhoku earthquake and tsunami struck Japan, Milligan decided to flee the country, fearing for the safety of not only himself, but his wife and child. With the
J2 League suspended until further notice, JEF United Chiba gave permission for Milligan to train in a bid to keep his fitness up with his former A-League club
Sydney FC.
Melbourne Victory in 2013 On 23 January 2012 it was reported that
Melbourne Victory was to secure Milligan on loan until the end of the
regular season. It was confirmed on 24 January that Milligan signed for a loan deal to Melbourne Victory until the end of the 2011–12 A-League season, becoming the first
Sydney FC player to switch to Melbourne Victory. He returned to Japan in March. In July 2012, Milligan was released from JEF United Chiba and returned to Melbourne Victory by signing a three-year contract. Milligan starred for Melbourne Victory during their 2012–13 season, moving from centre-back to play as a defensive midfielder, and quickly established himself as one of the best players in the league. Although he has never been a prolific goal scorer, Milligan scored 8 goals in this season, a number of them being clutch goals in important games, including a penalty equaliser in an elimination final against
Perth Glory that Melbourne Victory went on to win in extra time. To cap off his season, Milligan won the
Victory Medal, awarded to the club's player of the season. On 17 September 2013, Milligan was rewarded for his performances by being appointed the captain of Melbourne Victory, replacing
Adrian Leijer. He was also rumoured to be leaving Melbourne Victory to join fellow national team midfielder
Mile Jedinak at newly promoted
Premier League club
Crystal Palace, however Melbourne Victory rejected a rumoured
£2 million offer for the defensive midfielder. Milligan, after a trial at Crystal Palace, stayed on at Melbourne Victory as captain in the 2013–14 season. He sustained an injury halfway through the season, and the team suffered for this and other reasons such as losing their coach, an injury to Adrian Leijer (ex-captain and central defender) and four players (including three defenders) going to the Under 21 World championships (Jason Geria, Connor Pain, Scott Galloway and Nick Ansell). However, Victory improved after this period to finish fourth in the A-League. Milligan played every minute of all but one ACL match, only missing the final away match of the ACL Asian Champions League match through suspension. On 17 May 2015, Milligan captained his side during their 3–0 defeat of
Sydney FC in the
2014–15 A-League Grand Final, held at
AAMI Park, Melbourne, and was awarded the
Joe Marston Medal as the best player in the match.
Baniyas SC At the end of the 2014–15 season it was announced that
UAE Pro-League side
Baniyas SC had triggered the release clause of Milligan's contract with a $1 million transfer fee, and he signed with them on a two-year contract.
Return to the Victory On 31 July 2017, it was announced Milligan would return to the Victory on a one-year deal as a marquee player.
Al Ahli On 28 January 2018, Melbourne Victory sold Mark Milligan to Al-Ahli for $1 million. He was assigned the number 5 shirt. On 4 February, he made his debut for Al-Ahli in a league game against
Al Ittihad FC. He played at centre-half, with the game finishing 0-0. He got good response from the fans, playing the full 90 minutes in the
Jeddah derby.
Hibernian On 18 August 2018, Milligan signed a two-year contract with
Scottish Premiership club
Hibernian. Milligan played regularly for Hibernian during the 2018–19 season, after which he left the club. Hibernian head coach
Paul Heckingbottom said that he had opted to exercise a break clause in Milligan's contract as he wanted to "recruit something different to play in that position".
Southend United On 1 July 2019, Milligan signed for
Southend United. Milligan was released by Southend United on 19 June 2020, after the team's relegation from League One.
Macarthur FC On 30 July 2020, following his release from Southend, Milligan returned home to Australia to join newly formed
A-League club
Macarthur FC, signing a two-year deal. On 22 October, he was named the club's captain for their inaugural campaign in the A-League. In the club's first match, a local derby against
Western Sydney Wanderers on 30 December, Milligan scored the club's first goal which secured a first-ever win. On 2 June 2021, Milligan announced that he would be retiring from football at the end of the
2020–21 season and would join the coaching staff at Macarthur. ==International career==