After 2002 World Cup, Nakata played as defensive midfielder under new manager Zico. Although his opportunity to play decreased, he was elected Japan for many competition, 2003, 2005 Confederations Cup, 2004 Asian Cup and 2006 World Cup. At 2004 Asian Cup, he played 4 matches and scored 2 goals in semifinal and final, and Japan won the champions. He played 57 games and scored 2 goals for Japan until 2007.