Fujimoto was born in Yamato on March 24, 1984. When he played for University of Tsukuba, he joined J1 League club Shimizu S-Pulse in 2005. He was given number "10" shirt as Masaaki Sawanobori successor from the 2006 season. In the 2006 season, Fujimoto played 28 matches and scored 8 goals and was selected "Young Player of the Year award". The club won the 2nd place in the 2008 J.League Cup and 2010 Emperor's Cup. He was also selected Best Eleven in 2010. In 2011, he moved to Nagoya Grampus which won the J1 League champions in 2010 season. In 2011, the club won the 2nd place J1 League and he was selected Best Eleven. In 2014, he moved to Yokohama F. Marinos. Although he played many matches in 2014, his opportunity to play decreased under new manager Erick Mombaerts in 2015. In 2016, he moved to Gamba Osaka. From July 2019, he played for Kyoto Sanga FC and SC Sagamihara.