St. Stephen's Anglican Church was founded in 1986 by a merger of two Episcopalian house-churches, both dedicated to the orthodox worship and spirituality of the 1928 Book of Common Prayer: Holy Trinity Episcopal Church, established in a home on West Capitol Street on May 2, 1970; and an informal group that began meeting in the early 1980s in the Millsaps College Chapel, later relocating to the home of Freda Katool Holmes.

The unified congregation called the Rev. Walter Van Zandt Windsor as their rector and held their first services in the chapel at the Mississippi Agricultural Museum. On December 6, 1992, a newly-constructed church building was dedicated in Flowood. The congregation has worshiped here faithfully ever since.

Saint Stephen's is a member parish of the Diocese of Mid-America of the Reformed Episcopal Church (REC) since 2005 and of the Anglican Church in North America (ACNA) since its creation in 2009. She is under the episcopal oversight of the Rt. Rev. Ray R. Sutton.