McQualter was raised in Traralgon, Victoria, and attended Gippsland Grammar School and later Caulfield Grammar School as a boarder along with future St Kilda teammate Brendon Goddard. McQualter and Goddard both captained the school's First XVIII football team and played in the First XI cricket side.
McQualter captained the Victorian Country Under-16 and Under-18 teams at the National Football Championships. He was selected by St Kilda with the 17th overall selection in the first round of the 2004 AFL Draft.
McQualter was drafted by the St Kilda Football Club in the 2004 NAB AFL Draft - 1st round selection pick 17 overall.
McQualter debuted for St Kilda in Round 8 of the 2005 season against the West Coast Eagles at Subiaco in Perth, with 16 possessions.
He averaged 13 possessions per game over seven senior games in the 2005 season.
He appeared in 10n games in the 2006 season.
At the end of the 2007 season, McQualter had played 23 games, earning 137 kicks and 121 handballs, for a total of 258 disposals (an average of 11.2 possessions per game).
McQualter was officially delisted by the Saints at the end of the 2007 season, despite having another year to run on a two-year contract. He was reported as saying that he felt he had "stagnated" in his third year of football. He was then redrafted by the St Kilda Football Club onto the club's rookie list in the 2007 Draft and returned to the team.
McQualter began the 2008 season quietly on St Kildas rookie list, but began to turn in several solid performances with St Kilda's affiliate in the Victoria Football League (VFL). With his continued good form McQualter was temporarily elevated off the rookie list and selected to play against Sydney in Round 12. He cemented his place in the senior team after several tagging jobs and played nine consecutive games, a personal best for McQualter at the time.
He played his first AFL final in the 2008 1st Qualifying Final against Geelong.
McQualter was promoted back onto St Kilda's primary list at the end of the 2008 season.
McQualter played in 21 of 22 matches in the 2009 season in which St Kilda qualified in first position for the 2009 finals series, winning the club’s third minor premiership.
St Kilda won through to the 2009 grand final after qualifying and preliminary final wins. McQualter played in the 2009 AFL Grand Final in which St Kilda were defeated by 12 points.
McQualter averaged 14.4 possessions per game and kicked 22 goals in 24 matches during the 2009 season.
As of the end of the 2009 season, McQualter had played in six finals matches, including one grand final.
McQualter played 25 games in 2010, including four finals matches.
As of the end of the 2010 season, McQualter had played in 10 AFL finals matches, including three grand finals. He was delisted at the end of the 2011 season following the Saints' elimination final loss to the Sydney Swans.
McQualter joined the Gold Coast Suns' rookie list in 2012 and began playing in the Suns' North East Australian Football League reserves team. He was part of the Suns' leadership group and played in Round 8 of the AFL season.
McQualter joined Richmond as a development coach and will play in their VFL team in 2014.