Perrotta also represented the Italian national team during the 2006 FIFA World Cup under coach Marcello Lippi, starting in all seven of the "Azzurri"'s games, including the final, en route to their fourth World Cup title, setting up Filippo Inzaghi's goal in a 2–0 win over the Czech Republic in Italy's final group match of the tournament on 22 June. Unlike with Roma, Perrotta was often used as a left winger with the Italian national team under Lippi, or as a "front-lying" defensive midfielder, as he was in the 2006 World Cup.