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.