Fujita was born in Shizuoka on October 4, 1971. After graduating from University of Tsukuba, he joined newly was promoted to J1 League club, Júbilo Iwata in 1994. The club won the J1 League champions in 1997, 1999 and 2002. He was selected MVP in 2001 and "Japanese Footballer of the Year" in 2002. This was golden era in the club history and he was one of the central player in golden era. In summer 2003, he moved to Dutch Eredivisie club Utrecht on loan. In January 2004, he returned to Júbilo Iwata. However his opportunity to play decreased from 2005. In summer 2005, he moved to Nagoya Grampus Eight (later "Nagoya Grampus"). Toward the end of his career, he played for J2 League club Roasso Kumamoto (2009–2010) and JEF United Chiba (2011).