Nakamura has 98 caps and 24 goals for the Japanese national football team, including appearances in the FIFA World Cup finals in 2006 and 2010 and winning the AFC Asian Cup in 2000 and 2004; he was named Most Valuable Player of the 2004 competition. He also appeared in the 1997 FIFA World Youth Championship as a member of the Japanese Under-20 team and the 2000 Summer Olympics as a member of the Japanese Under-23 team.