Nakata was born in Otsu on July 9, 1979. After graduating from Teikyo High School, he joined J1 League club Kashima Antlers in 1998. Japan national team players Masashi Motoyama, Mitsuo Ogasawara and Hitoshi Sogahata are Nakata's contemporaries. He debuted as defensive midfielder in first season and the club won the champions 1998 J1 League. From 2000, he became a regular player and constituted midfielder with Yasuto Honda, Bismarck, Motoyama and Ogasawara. In 2000, the club won all three major title in Japan J1 League, J.League Cup and Emperor's Cup. In 2001, the club won J1 League and he was also elected Best Eleven. the club also won 2002 J.League Cup. Nakata moved from Japanese giants Kashima Antlers to France at the start of 2005 when former Japan national team manager Philippe Troussier, then the Olympique 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 by early 2006 had moved to Switzerland's top team Basel where he played as a defender. Nakata returned to Kashima Antlers in July 2008. He played at many defensive position, defensive midfielder, left side-back and center-back. The club won the champions 2008, 2009 J1 League, 2010 Emperor's Cup, 2011 and 2012 J.League Cup. He retired end of 2014 season.