Thompson made his first international appearance for Australia on 28 February 2001 in a friendly match against Colombia. He then was included by coach Frank Farina in the squad for the 2002 FIFA World Cup qualification matches played in April 2001. On 9 April 2001, he came on as a substitute and scored his first international goal in Australia's first match against Tonga, which Australia easily won 22–0, breaking the world record for the largest win in an international match. Two days later, in the match against American Samoa, Thompson was named as starter with regular attackers either rested or omitted from the squad. Australia went on to break their own record by winning 31–0, with Thompson scoring 13 goals, breaking the world record for most goals scored in an international match. American Samoa, who had player eligibility issues, fielded a team with youth players and was not a match to Australia, even though Australia themselves were missing several star players.