Although Nakata played as defensive midfielder at the club, he played as left-back of three backs defense at U-20, U-23 and Senior national team under manager Philippe Troussier. In April 1999, Nakata played for U-20 Japan at 1999 World Youth Championship. He played all 7 matches with defender Kazuki Teshima and Shigeki Tsujimoto, and Japan won the 2nd place. On February 5, 2000, Nakata debuted for Japan national team against Mexico. In September, he was selected U-23 Japan for 2000 Summer Olympics. Although he played as regular player, he got hurt in third match against Brazil and he could not play after the match. In 2001 and 2002, Nakata played all matches for Japan including 2001 Confederations Cup and 2002 World Cup. At Confederations Cup, Japan won the 2nd place. At 2002 World Cup, he played full-time all 4 matches. After 2002 World Cup, Nakata played as defensive midfielder under new manager Zico. Although his opportunity to play decreased, he was elected Japan for many competition, 2003, 2005 Confederations Cup, 2004 Asian Cup and 2006 World Cup. At 2004 Asian Cup, he played 4 matches and scored 2 goals in semifinal and final, and Japan won the champions. He played 57 games and scored 2 goals for Japan until 2007.