Newcastle Jets He scored a spectacular goal against Central Coast Mariners in Legal 2 of the 2005-2006 semi-finals. He scored a similarly spectacular goal in Round 20 of the 2006-2007 season against Adelaide United. On 20 December 2008 he scored a hat trick, against Melbourne Victory at EnergyAustralia Stadium in their shock 4-2 upset victory.
Thompson was made captain of the Jets in the 2009-2010 due to a new Newcastle Jets policy that the player who has the most top-flight appearances for the club would receive the captain"s armband.
Melbourne Heart On 24 November 2009 he signed a contract with 2010-2011 A-League expansion club, Melbourne Heart, becoming one of the club"s first signings. Thompson is the record games holder for the Aleague. captained the club under Dutch international John Van Schip.
As a result of the Heart finishing second-to-last on the A-League ladder, their worst finish in an A-League season, Thompson, along with teammates Simon Colosimo, Clint Bolton and Fred, were released by the Heart at the conclusion of the 2012-2013 A-League season. Sydney Football Club On October 11, 2013, he signed with Sydney Football Club as an injury replacement for Peter Triantis.
He made his debut on the same day in Round 1 of the 2013-2014 season against Newcastle Jets.
Thompson made his first senior international debut for the Socceroos on 28 January 2009 in an AFC Asian Cup qualifying match versus Indonesia.