In February 2000, Nakamura was selected the Japan national team for 2000 Asian Cup qualifier. At this qualifier, he debuted against Singapore on February 13. He played many matches as regular player in 2000. He was also selected the Japan U-23 national team for 2000 Summer Olympics. In October, he played at 2000 Asian Cup and Japan won the champions. However he could hardly play in the match from 2001 and he was not selected Japan for 2002 World Cup. After the 2002 World Cup, he became a regular player under new manager Zico and played as central player for Japan for a long time. In 2004, he participated in the 2004 Asian Cup which Japan the champions. He played all 6 matches and scored 2 goals, and he was selected MVP award. He was selected Japan for 2006 World Cup. He played all 3 matches and scored 1 goal. In 2007, he played in the 2007 Asian Cup, but this time the team failed to defend the title and finished the 4th place. In 2010, he was selected Japan for 2010 World Cup. However he lost his position just before 2010 World Cup and he played only one match as substitute. After the 2010 World Cup, Nakamura retired from national team. He played 98 games and scored 24 goals for Japan.