According to church history, Jenkinsburg Missionary Baptist traces its origins to County Line Baptist Church, organized in 1861. For many years, services were held in an old schoolhouse until a church building was erected in 1886.

The small farming community of Jenkinsburg developed under the leadership of William H. Jenkins (1826–1899), a Confederate veteran who settled in the area after the Civil War. He married Nancy Crumbley in August 1865 and became a driving force in the town’s growth. In 1881, Jenkins deeded a strip of land for the construction of a new railroad line, which helped spur development. The town was officially incorporated as Jenkinsburg in 1889.

In 1910, C. L. Carter proposed moving County Line Baptist to Jenkinsburg. Two years later, in 1912, several members withdrew from County Line and organized Jenkinsburg Missionary Baptist Church with 22 charter members. The first meeting was held on April 26, 1913, and the congregation quickly began work on a permanent home. The new sanctuary was completed and formally dedicated on May 30, 1915, marking the beginning of a new chapter for the community’s Baptist worship.