On October, 2006, Nakamura debuted for the Japan national team against Ghana. After the debut, he played many matches as offensive midfielder and defensive midfielder. In 2007, he participated at 2007 AFC Asian Cup and played all 6 matches. However his opportunity to play decreased from spring 2010. He was selected Japan for 2010 World Cup and played 1 matches as substitute midfielder. In 2013, he played at 2013 Confederations Cup. This tournament is his last match for Japan. He played 68 games and scored 6 goals for Japan until 2013.