On 12 October 2004, he was recalled to the team and made a substitute appearance in the 2004 OFC Nations Cup final, which Australia won. Since then, Thompson was more regularly called up to the national team, although most of his appearances were as a substitute. He was also included in Australia's squad for the 2005 FIFA Confederations Cup, appearing in two matches as a substitute. In 2005, Thompson returned to Australia to play for Melbourne Victory in the inaugural A-League season. Despite not playing in Europe, he retained his place in the national team and became the only A-League based player in Australia's squad for the qualification matches against Uruguay for a berth in the 2006 FIFA World Cup. Australia eventually qualified for the 2006 World Cup. His good form for Melbourne earned Thompson a place in Australia's squad for the World Cup. He was one of three A-League based players in the squad, even though he spent the run-up to the tournament on loan at PSV Eindhoven. However, he did not receive any playing time in the tournament, as Australia was eliminated in the second round.