After having represented U-17 Japan at the 1993 U-17 World Championship (where he scored a goal) and U-20 Japan at the 1995 U-20 World Championship (where he scored twice), Nakata was part of the U-23 Japan squads at the 1996 Olympics, where Japan upset Brazil, and at the 2000 Olympics. His senior national team debut came in May 1997 against South Korea.