Nakamura was first selected for the Japan national team in 2006 under Ivica Osim and earned his first cap on 4 October in a 1–0 friendly win against Ghana.

After battling through injury, he was named in the Japan squad for the 2010 FIFA World Cup, making one substitute appearance as the side reached the round of 16.

"[1] The following year, He was named club captain and led Chuō to win the 2nd Division, earning promotion back to the top league at the first time of asking.

Nakamura's work as club captain at Chuō had attracted attention from J League scouts, and he was invited for a trial by Kawasaki Frontale of the Second Division shortly after graduation.

[1] He made his first appearance on the opening day of the 2003 Division 2 season against Sanfrecce Hiroshima, coming on in the 88th minute to replace Takehito Shigehara.

Continuing to play as a starter, Nakamura's first season in the First Division was a modest success, making 29 appearances and scoring 2 goals as Frontale managed to safely avoid any threat of relegation with an 8th place finish.

Nakamura continued to hold down his starting place in central midfield, scoring 10 goals as the ambitious Frontale became serious challengers for their first ever First Division trophy.

Despite falling short to Urawa Red Diamonds and finishing second, the 2006 season was seen as one of many positives for the side and considered to be Nakamura's best yet, as he scored 10 goals from midfield and was named in the J League Best XI along with teammate Hiroyuki Taniguchi, marking the first time any Frontale players had been included.

[4] Nakamura was injured during an AFC Champions League game against Seongnam Ilhwa on 23 February 2010, suffering a Mandibular fracture, casting doubt over his eligibility for selection in the upcoming 2010 FIFA World Cup; Nakamura was however able to make a speedy recovery and was named in Japan's squad, but only made one substitute appearance as Japan were knocked out in the round of 16.

The following season saw him placed in a prolific three man attacking partnership with new signings Yoshito Ōkubo and Renatinho, with Nakamura providing 7 goals and 8 assists as Frontale earned a return to the AFC Champions League for the first time in three years.

Despite this, Nakamura's efforts were recognised as he was named both J League MVP and Japanese Footballer of the Year, becoming the oldest recipient of either award at the age of 36.

He was recognised as a highly efficient passer of the ball, regularly topping the J League for assists throughout his career, as well as being a consistent goal threat and an adept dribbler with determination and strength, despite his relatively small size.