The first match played in the hills was between Macclesfield and Gembrook in 1894. In 1895, Gembrook defeated Pakenham by 6 goals.

The Gembrook Football Club was officially formed in 1906, participating in the Evelyn Football Association. Football games were suspended during WW1, with the club reforming in 1919. In this year the MDFA was formed and Gembrook FC was one of the founding clubs. When the YVMDFL was formed in 1966, Gembrook FC was again one of the original member clubs.

The junior club was founded in 1972 as part of the senior club. The junior club moved to the Mountain Rd Reserve at Cockatoo in 1996, and changed its name to Gembrook-Cockatoo.

The senior club changed its name to Gembrook Cockatoo in 1997.