Following the relocation of Clarendon along the railroad in 1887, the African American population began to grow. By the 1890s, African Americans were searching for their own place of worship in the growing community. For a time, they gathered in private homes of met under a shade tree to read bible verses. While riding the combination train into Clarendon, a young African American cowboy, Matthew "Bones" Hooks (1867-1951), meet reverend Sid Stephens and persuaded him to help organize a church for the African American population. A location was found in an empty shelter in 1897 and Rev. Stephens gave the new church his name and stayed on as pastor. Bones Hooks also remained in Clarendon and helped build St. Stephens before he married and moved to Amarillo. Pastors included Rev. Stephens, Rev. L.G. Farley and Rev. A.G. Monagram.
In May 1918, the church building was destroyed by a massive flood. However, under the leadership of rev. Pickford, the congregation found a new location and in spite of declining membership, the church remained strong. In 1930, Rev. J.J. Hayden organized the first choir who sang at church services and performed for the public on special occasions. In the 1940s, a building was moved from Lelia Lake to Clarendon to be used by St. Stephens. During the next thirty years, the congregation held
many fundraisers to support the church and celebrate its heritage. The old schoolhouse was purchased for the Pastor's home and a baptistery was added to the church. As the first African American church in the Panhandle, St. Stephens Baptist Church has survived for more than a century due to the determination of the congregation and the community.