He has played for Shimizu S-Pulse, Nagoya Grampus, Yokohama F. Marinos, Gamba Osaka, Kyoto Sanga, SC Sagamihara and the Japan national team.

Fujimoto was educated at and played for Toko Gakuen High School, during which time he was also a member of the Japan national U-17 team for the 2001 FIFA U-17 World Championship hosted by Trinidad and Tobago.

After graduating high school Fujimoto received an offer from J2 League side Kawasaki Frontale, but he decided to continue his studies and play football at the University of Tsukuba.

He was seriously injured in late season of 2008 and made a comeback goal against Kyoto Sanga FC via direct free kick on 19 August 2009.

He signed for Gamba Osaka ahead of the 2016 season and in his first 3 years at the club he was never able to establish himself as a first-team regular for any sustained period of time.

His next international involvement came when he made brief second-half appearances in both matches in Japan's double header in June of that year, the 2-0 win over Montenegro and the 0-0 draw with Colombia.