Nakata was selected the Japan U-23 national team for 1996 Summer Olympics. In first match against Brazil and Japan won Brazil (1-0). It was known as "Miracle of Miami" () in Japan. On May 21, 1997, he debuted for the Japan national team against South Korea. After the debut, he became a regular player soon. In 1998, he was selected the Japan at 1998 World Cup and played all 3 matches. In 2000, he was selected U-23 Japan for 2000 Summer Olympics. He also played at 2002 and 2006 World Cup. He played 77 games and scored 11 goals for Japan until 2006.
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