The current club was formed in 2010 as a merger of two clubs, Fujieda Nelson and Shizuoka FC. The My Football Club project bought Fujieda Nelson CF in 2008 and renamed them Fujieda MYFC. Then in 2010, My Football Club bought Shizuoka FC and merged the two clubs to form Shizuoka Fujieda MYFC and appointed Toshihide Saito as player/manager of the club. 
On 2011, they took second place in the Regional Promotion Series and therefore won promotion to the Japan Football League for the first time, becoming the third representative of the prefecture in the national leagues. They then dropped the Shizuoka from their name and become just Fujieda MYFC.
In 2012, the club finished their first season in the Japan Football League in 11th place and therefore secured their place in the division for the following 2013 season.
Fujieda play their home games at two different stadiums, with home matches split between the two grounds. One of the stadiums is the Fujieda Sports Complex Park which has a capacity of 13,000. The other stadium is the Fujieda Citizen Ground, which was opened in 1967 and has a capacity of 3,000.