Immanuel Baptist Church was first known as the North Augusta Baptist Mission.  The first meeting of the mission was held on July 4, 1954 with 35 residents, along with interested friends and members of  First  Baptist Church of North Augusta.  Services were conducted by the North Augusta Baptist Church until October 9, 1954 when Rev. L. H. Fowler was called as pastor.

On February 6, 1955 the North Augusta Baptist Mission was constituted as the Immanuel Baptist Church with 104 charter members and Rev. L. F. Fowler as pastor.

The acre of land on which the mission was built was donated by Mrs. R. A. Toole, Sr., in memory of her mother Mrs. Ellen Benson Toole.  Additional lots have been purchased since then.  The first building occupied was an army barrack purchased from Fort Gordon.  On June 6, 1956 the church voted to build its first educational building and temporary auditorium.  The building was completed and dedicated on June 9, 1957.  In September of 1962 the church entered into a $140,000 bond issue and consolidation program to pay off total indebtedness of the church and to construct a new auditorium and educational space.  The first service in the new sanctuary was held on April 7, 1963, and the dedication service was held on April 21, 1963.  On September 22, 1976, the Church accepted the proposed floor plan for the new educational building and to locate the building alongside the auditorium.  The dedication service for the new educational building was held on November 13, 1977. 

The church held its 60^th Anniversary on September 27, 2015.