The Yugoslav team was renamed Serbia and Montenegro by the time 2006 World Cup qualifying started, and Stanković started in all games and scored two goals, but missed the last qualifier through injury. At the 2006 FIFA World Cup, he was given the number 10 shirt and Savo Milošević captained the new Serbia and Montenegro team in their first World Cup, but they failed to progress to the knock-out rounds after losing all their group matches to the Ivory Coast, Argentina and the Netherlands. After Milošević retired, the midfielder took over as captain of the re-formed Serbia national team, following the breakup of Serbia and Montenegro.