Fujimoto was born in Ube on October 31, 1977. After graduating from Tokushima Municipal High School, he joined J1 League club Avispa Fukuoka in 1996. He played many matches in 1998. He moved to Sanfrecce Hiroshima in 1999. The club won second place in the 1999 Emperor's Cup. However the club was relegated to the J2 League in 2002. After that, although he played for Nagoya Grampus Eight in 2003 and Vissel Kobe in 2004, his opportunity to play decreased. In 2005, he moved to Omiya Ardija. He played central player at the club and also served as captain. He moved to Roasso Kumamoto in 2012. He retired at the end of the 2014 season.