In January 2000, after one and a half seasons at Perugia, Nakata moved to Roma for 42 billion lire helping the team win the scudetto. The highlight of Nakata's career at Roma came on 6 May 2001 in the Serie A match against Juventus at Stadio Delle Alpi. After replacing Francesco Totti in the second half with Roma trailing 0–2, Nakata netted with a 30-yard goal beyond Juventus goalkeeper Edwin van der Sar's reach, with 11 minutes left in the match. He then helped Roma score the equalizer when his fierce drive from outside the box was parried by Van der Sar into the path of Vincenzo Montella, who scored for Roma in the last minute. The match ended with a 2–2 draw and Roma maintained a six-point margin at top of the league table.
Despite Nakata playing every match in Japan's first three World Cup appearances, he was not selected for the country's Asian Cup-winning squads in 2000 and 2004. In total, he was capped 77 times for Japan, scoring 11 goals, 9 of which came in official FIFA competitions.