At age 12 in 1991, Nakamura joined the youth setup of Nissan Motors F.C. [ja], one of the predecessors of the club known today as Yokohama F. Marinos. While training at the youth setup, Nakamura was already honing his dead-ball technique, practicing free kicks for an hour every day outside of team practice; his coaches also acknowledged he had good ball skills and technique. However, at that time Nakamura was physically underdeveloped compared to his teammates and struggled to transition to the youth level, and eventually was not chosen for the youth team.

Rather than continue on the fringes of Nissan’s youth setup, Nakamura instead decided to enroll at Tōkō Gakuen High School [ja] in Kawasaki, despite the school being a two-and-a-half-hour commute each way. Nakamura led Tōkō Gakuen to Japan’s national high school football tournament in 1995 and to the tournament final in 1996. It was his performance there that earned him a call-up to the Japanese Under-20 team for the 1996 AFC Youth Championship and subsequently for the 1997 FIFA World Youth Championship.

Nakamura’s national team career with Japan started in 1996 as the only high school player selected to the Under-19 team for the Asia Youth Championship. The following year, he was a member of Japan’s Under-20 team that finished in the final 8 of the 1997 World Youth Championship.

By his graduation from Tōkō Gakuen in 1997, Nakamura had attracted interest from several top-flight Japanese clubs, including offers from Júbilo Iwata, Verdy Kawasaki, and Gamba Osaka.

In 1997, Nakamura chose to sign with J.League Division 1 club Yokohama Marinos, the club whose youth setup he had left only a few years earlier. Nakamura made his début with Marinos on 8 March in an J.League Cup match against Verdy Kawasaki and his league début on 16 April against Gamba Osaka. Nakamura finished his rookie season with 31 appearances and 5 goals.

Nakamura had his breakout season the following year in 1998, making 37 appearances and scoring 10 goals; his playmaking ability in creating scoring chances for teammates also contributed to Nakamura being considered one of the best young players in Japan. In 2000, Nakamura had his best season in Yokohama, recording 5 goals and 11 assists in league play, helping Marinos to the first-stage championship; Nakamura was awarded J.League Most Valuable Player for his contributions. The following year, Nakamura made 31 appearances and scored 5 goals in all competitions, including 6 appearances and 2 goals in the 2001 J.League Cup, which the Marinos won.

In 1999, Nakamura was selected a member of Japan’s Under-23 team that won all its Asian qualifying matches in the run up to the 2000 Olympic Games in Sydney. Nakamura formed a lethal combination in the attacking midfield with Shinji Ono on a team that would form the core of the Japanese national team, and included Atsushi Yanagisawa, Junichi Inamoto and Naohiro Takahara. In Sydney, Japan reached the quarterfinal round.

Nakamura made his senior national team debut on 13 February 2000, in an Asian Cup qualifier match against Singapore. He scored his first national team goal against Brunei in the very next match on 16 February 2000, also in Asian Cup qualifying.

After playing a key role in Japan’s championship at the 2000 Asian Cup, Nakamura appeared to have cemented his place in the national team, having played every match of the tournament. However, his national team career took a sharp turn in a friendly match on 25 March 2001, a humiliating 5–0 loss to France. He did not play for the team led by manager Philippe Troussier again until almost a year later, in a friendly match against Ukraine on 21 March 2002.

Nakamura struggled with injuries in 2003 and was limited to just 18 appearances in the 2003–04 season (these injuries also caused him to miss a 2003 Confederations Cup game against Colombia and national team duty in November 2003). Additionally, Reggina underwent four managerial changes in just Nakamura’s first two years at the club; Walter Mazzarri, hired in the summer of 2004, would already be Nakamura’s fifth manager at Reggina. The frequent changes resulted in Nakamura mostly coming off the bench during the 2003–04 season and not fitting in well under Mazzarri in 2004–05 when Reggina only scored 36 goals in their entire league campaign, with Nakamura only managing to contribute two goals (although each came in crucial 1–0 league victories in a season where Reggina finished only 2 points clear of the relegation zone). Coupled with Reggina’s struggle to avoid relegation every season that he had been at the club, Nakamura became concerned he was regressing from top level football and decided it was time to move on.

Zico has lauded Nakamura’s improvement since 2002, especially his physical development, stating, “Unquestionably, he has improved a great deal since his move to Serie A. He is the soul of our midfield.” Nakamura has flourished under Zico’s attacking style and earned his place as the central playmaker. He led Japan to the championship at Asian Cup 2004, where he was named Most Valuable Player, and qualification for the 2006 World Cup Finals. Nakamura also starred for Japan in the 2003 and 2005 Confederations Cup, scoring a total of 4 goals in 5 matches.

Nakamura married a former Japanese talent in 2004. In the same year, his first son was born. His second son was born on 15 January 2008 in Glasgow, Scotland. According to the Evening Times, he is a fan of the Grand Theft Auto and Gran Turismo video games. He has appeared on the front cover (some of them with Zico) of the Japanese releases of Konami’s Winning Eleven video game series (WE 5 WE 9, WE 9: Ubiquitous Evolution and WE 10) in 2001, 2005 and 2006. He also appeared on the front cover of Namco’s Football Kingdom Trial Edition in 2004. He is the paid promoter of the Yamada electronics chain. His current boot sponsor is Adidas. Nakamura has illustrated the precision of his free kicks with novelty performances on television, including knocking ornaments off a wedding cake without disturbing the cake itself and striking a ball through the window of a moving bus.

New manager Gordon Strachan became interested in acquiring Nakamura due to his national team appearances in the 2005 Confederations Cup, in particular for his performance against Brazil in which Nakamura scored a goal and helped Japan to a 2–2 draw. The deal with Celtic was completed on 29 July 2005 for a reported transfer fee of £2.5 million, although Strachan has claimed the actual fee was far lower; part of the discrepancy may be due to the deal involving Celtic securing the player’s image rights with a view to enhancing the club’s profile and merchandising sales in the Far East. In welcoming Nakamura to the club, Strachan stated that Nakamura “has got imagination and he sees passes other people can’t see.”

Nakamura was suspended for the World Cup qualification match against North Korea on 8 June 2005 that clinched Japan’s place in the 2006 Finals, he nonetheless played a key role in the qualifying run and had replaced Hidetoshi Nakata as the main playmaker in Japan’s attack during that period.

In the 2006 FIFA World Cup Nakamura scored the controversial opening goal in Japan’s first game against Australia, which Australia came back to win 3–1.

Nakamura featured little in the first part of Celtic’s 2007–08 campaign due to a knee injury which was initially picked up in a Champions League qualifying match against Spartak Moscow in August 2007. Nakamura attempted to play through the injury, including coming on as an 85th-minute substitute in a Champions League group stage match against A.C. Milan and being involved in the buildup to Scott McDonald’s injury time winner. However, Nakamura wound up repeatedly aggravating the injury, including in a match against Motherwell on 27 October, after which an MRI revealed nerve damage next to a knee ligament and Nakamura sat out for nearly three months. During this time, Celtic slipped from the top of the table into second place; teammate Artur Boruc called Nakamura’s absence the “big difference” in Celtic’s drop in form. Nakamura returned to play on 12 January, for Celtic’s Scottish Cup match against Stirling Albion, in which he scored a goal.

On 28 February 2009, he scored a hat trick against St Mirren in a 7–0 win.

After the 2010 World Cup, Nakamura retired from international football.

In 2011, Nakamura was appointed captain of Marinos and led the club to its best point total (56) since Marinos last won the league in 2004.

During the 2013 season, Nakamura made 33 appearances and scored 10 goals in league play. He also made 10 appearances and scored 2 goals in the 2013 Emperor’s Cup, which the Marinos won. His league goal tally included a free kick goal against Oita Trinita on 27 October, Nakamura’s 17th direct free kick goal in J1 League, surpassing Yasuhito Endo for the all-time league record. However, Nakamura was sidelined with injury late in the season and the Marinos lost three of their final four games, finishing one point behind Sanfrecce Hiroshima in the title race. Nakamura described Marinos’ collapse as the “worst moment” of his career. Nevertheless, Nakamura was awarded J.League Most Valuable Player for his contributions, becoming the first and only multiple-time winner and, at the time, the oldest recipient of the award.

After the end of the 2016 season, J1 League rivals Júbilo Iwata made a multi-year contract offer to Nakamura. This led to media speculation in December that Nakamura was unhappy at Marinos due to interference in both player and staff personnel decisions by City Football Group, who had taken a 20% stake in Marinos in 2014. Júbilo Iwata confirmed signing Nakamura on 8 January. Nakamura reiterated his desire to retire with boyhood club Marinos – the only club he had played for in J.League – and expressed disappointment that he never won a league title with Marinos, but cited the ongoing stakeholder interference as creating an atmosphere where “every day there were things I felt were wrong” and he could not “face football properly”. Nakamura reportedly accepted an annual wage of ¥80 million from Júbilo Iwata despite a contract extension offer from Marinos worth ¥120 million annually. Marinos general manager Takao Toshishige [ja] publicly expressed regret at the club’s failure to re-sign Nakamura, saying “We absolutely cannot allow something like this to happen again.” A Marinos official reportedly stated that due to Nakamura’s popularity with fans, his departure could result in a one-third drop in Marinos annual revenue.

During the 2016 season, Nakamura became the longest-serving captain in Marinos history, passing Masami Ihara. He also scored free kick goals against Avispa Fukuoka on 5 March and against Gamba Osaka on 2 April, his 21st and 22nd direct free kick goals in J.League, further extending the all-time league record.

Nakamura joined Júbilo Iwata for the 2017 season. He scored his first goal for Júbilo in a match against Omiya Ardija on 11 March, scoring from a direct free kick to bring his record J.League tally to 23; the goal was later nominated for J.League Goal of the Month for the February–March period. Nakamura followed up the nomination by winning J.League Goal of the Month for April for his 30-yard strike against Kashima Antlers on 22 April. However his opportunity to play decreased in 2018 season. In 2019 season, he played only 2 matches until July.

On 11 July 2019, Nakamura moved to J2 League club Yokohama FC. Nakamura made six appearances in the 2019 season, scoring one goal as Yokohama went on to win promotion back to the J1 League.