Nakamura was born in Yokohama on June 24, 1978. After graduating from Toko Gakuen High School, he joined J1 League club Yokohama Marinos (later "Yokohama F. Marinos") in 1997. He played as regular player from first season. In 2000, the club won the 2nd place in J1 League. He was selected "J.League MVP" and "Japanese Footballer of the Year". In summer 2002, he moved to Serie A club Reggina. In 2005, he moved to Scottish Premier League club Celtic. The club won the champions 3 times in 2005/06, 2006/07 and 2007/08. In 2007, he was selected "Scottish Player of the Year" award. In 2009, he moved to Spanish La Liga club Espanyol. In February 2010, he returned to Japan and joined his first club Yokohama F. Marinos. In 2013, the club won the 2nd place in J1 League and he was selected "J.League MVP" and "Japanese Footballer of the Year". In 2017, he moved to Júbilo Iwata. In 2019, he could hardly play in the match and moved to J2 League club Yokohama FC in July. The club won the 2nd place in 2019 and was promoted to J1 from 2020.