Baptist families were among a group of some 4500 British emigrants that left England for South Africa in 1820. Upon their arrival in South Africa, William Miller (1779–1856) was appointed their religious leader. It was through his founding work that the first Baptist chapel was built in Grahamstown in 1823. The first ordained Baptist preacher to travel to South Africa was William Davies, who was sent by the Baptist Missionary Society in England. He arrived in 1832 and ministered in Grahamstown for a short period. Work in Kariega, about 16 miles from Grahamstown, began in 1834. A German settlement around 1860 brought the first German Baptist work led by Carsten Langheim. A German pastor, Carl H. Gutsche, baptized J. D. Odendall, who founded the first Dutch-speaking Baptist church in South Africa in 1886. The Baptist Union was founded in 1877 by four English-speaking churches and one German-speaking church. The South African Baptist Missionary Society was formed in 1892. Black Baptist churches united to form the Bantu Baptist Church in 1927, under the auspices of the South African Baptist Missionary Society.
The organization of the BUSA is made up of seven regional associations: Border Baptist Association, Baptist Northern Association, Eastern Province Baptist Association, Free State Baptist Association, Natal Baptist Association, Northern Cape Baptist Association, and Western Province Baptist Association.