John and Nancy Leakey became the first settlers in the Frio River Canyon area in 1856 when they established a home and sawmill nearby. The congregation originated in worship services held in the Leakey home by Methodist circuit riding minister H. G. Horton. In 1883 the Methodist congregation began meeting in a schoolhouse built in the newly established town of Leakey, and by 1885 the schoolhouse also housed a church school known as the Floral Sabbath Sunday School supervised by Dr. F. D. Johns. After J. B. and Fannie (Leakey) Johnson donated a town lot in 1890, the Leakey Methodist Episcopal Church, South, built its first sanctuary there in 1890-91. The congregation later met in the original sanctuary and the county courthouse before building a new sanctuary at this site in 1922. It became the Leakey Methodist Church in 1939, added an education building in 1955 and a new parsonage in 1965, and has continued traditions such as annual Easter sunrise services, community Thanksgiving services every three years, youth and senior programs, missionary efforts, and religious guidance for the community.