Born in New Zealand Thompson moved to Australia at an early age. He played for Gippsland Falcons, Carlton and Marconi Stallions in the Australian League before moving to Belgium to play for Lierse SK in 2001. Thompson made his debut for the Australian under-21 side in 1998 and for the senior Australia team in 2001. Although never a regular first-choice forward for the national team he was a member of the Australian squad at the 2006 World Cup, the 2007 Asian Cup and the FIFA Confederations Cups of 2001 and 2005 as well as the Beijing Olympics. Thompson does have one very important claim to fame. In the 2002 World Cup qualifying tournament, Oceania section, Australia defeated tournament debutants American Samoa by a world record 31-0 and Thompson set his own world record by scoring 13 of the 31 himself. He returned to Australia in 2005 and signed for Melbourne Victory.
Australia