Kangaroo Flat Baptist Church was first known as Kangaroo Flat Baptist Fellowship. It commenced with three families on February 1, 1976, meeting first in a home and later in the Kangaroo Flat Y.M.C.A. building. It was recognised as a Baptist Fellowship on September 9, 1977.
As the fellowship grew, it moved to Scots Church under the guidance of a part time Pastor. It was constituted as a Church with the Baptist Union of Victoria on December 7, 1980 with approximately 29 members.
The existing building was purchased from the Uniting Church on June 2, 1986 and an extension that added the kitchen and toilet areas was completed in 2002.
Construction of the new multi-use building which functions as the main worship centre and can also be used for other functions was completed in early 2019.