Farmdale Baptist Church began through an interdenominational Sunday School movement, initated by St. John's Evangelical Church and held at the old Prestonia 36th District School, which stood at the modern junction of the Watterson Expressway and Preston Highway. On September 7, 1922, a Baptist minister named William R. Manion from Grace Baptist Church led a meeting which called for starting a new Baptist church from the Sunday School crowd. In March 1923, Manion was ordained by Grace Baptist and called to lead this new congregation, and a the group purchased a lot on the northeast corner of Preston and Farmdale Avenue. A building was put in place in September of that year, and the church was formally constituted on September 27, 1925. The church moved to its present location in January of 1975, and the old building was demolished to make way for improvements to the Watterson.

Bethlehem Baptist Church (1939) and Green Acres Baptist Church (1953) are church plants of Farmdale Baptist Church.