At international level, he represented Japan national team playing at both the 2002, and the 2006 FIFA World Cup.

Japan national team players Masashi Motoyama, Mitsuo Ogasawara and Hitoshi Sogahata were Nakata's contemporaries.

From 2000, he became a regular player and constituted midfielder with Yasuto Honda, Bismarck, Motoyama and Ogasawara.

Nakata moved from Japanese Kashima Antlers to France at the start of 2005, when former Japan national team manager Philippe Troussier, then the Olympique de Marseille coach, signed him in a deal.

After an understandably unhappy season in France (Troussier was sacked just a few months later), the frozen-out Nakata jumped at the chance to leave and early 2006 he moved to Switzerland's top team FC Basel.

[5] Just one week later he scored his first goal for his new club on 26 February, also in a home game, it was the equaliser after Basel fell behind and eventually the team won 2–1 against Yverdon-Sport.

A last-minute goal from Zürich's Iulian Filipescu meant the final score was 1-2 in favour of the away team and it gave FCZ their first national championship since 1980–81.

In the second qualifying round they were drawn against FC Vaduz from Liechtenstein, narrowly progressing on the away goals rule after a 2–2 aggregate draw.

At home against AS Nancy the match was drawn 2–2 and the final game ended with a 3–1 defeat against Wisła Kraków.

[9] At the end of the 2006–07 Super League season Basel were runners-up, one point behind championship winners Zürich.

Winning both matches in the qualification round and both matches in the play-off round, they team advanced to the group stage, which they ended undefeated in second position, after playing 1–0 at home against Stade Rennes, 0–0 away against Dinamo Zagreb, 1–0 at home against Brann and 1–1 away against Hamburger SV, to continue the knockout stage.

[13] In the Swiss Cup via FC Léchelles, SC Binningen, Grasshopper Club, Stade Nyonnais and in the semi-final Thun, Basel advanced to the final, and winning this 4–1 against AC Bellinzona they won the competition.

He played all 7 matches with defender Kazuki Teshima and Shigeki Tsujimoto, and Japan won the 2nd place.

At 2004 Asian Cup, he played 4 matches and scored 2 goals in semifinal and final, and Japan won the champions.