He was a key member of the Japanese side that qualified for the 1998 World Cup, scoring five goals in qualification matches and setting up all three Japanese goals in the qualification play-off against Iran. He helped Japan reach the final of the 2001 Confederations Cup but left the national team before the final to join Roma for their final league matches. Nakata played in all four of Japan's matches at the 2002 World Cup, co-hosted by South Korea and Japan, scoring the second goal of a 2–0 first round win against Tunisia.