He attended and played football at Shimizu Commercial High School(清水商業高校,Shimizu Shōgyō Kōkō?) and University of Tsukuba before joining Jubilo Iwata in 1994. Playing as a creative midfielder, Fujita has played an integral role in helping to build Jubilo Iwata into one of the most successful franchises in the J. League.
Although Fujita is not as well known as some of his more illustrious teammates, this probably has more to do with his low-key manner and quiet efficiency rather than a lack of skills. As part of the Jubilo midfield, Fujita had an essential role in providing the transition from defense to attack. In 1999, his contributions to his team were finally recognized as he was made team captain and won the league MVP award.
Fujita joined FC Utrecht, a team of the Eredevisie, on loan in mid-2003. The team was unable to match the performances of the top-tier teams in the Netherlands. As a result, FC Utrecht were unwilling to pay the transfer fee required to keep Fujita and he returned to Japan to once again play for Jubilo Iwata at the end of 2003.