St. Francis of Assisi Episcopal Church had its beginning in 1939 when a small group of Episcopal Church members of the Prairie View A. & M. College community met to discuss the formation of an Episcopal congregation in Prairie View, Texas.  Miss Maude Ernestine Suarez, Dean of Women at the college was a leading member of this group that worked during the succeeding decade of the 1940's to establish a permanent Episcopal chaplaincy and congregation at Prairie View. The congregation met in the Guest House Building on the Prairie View campus.

In 1950, this group realized its ambition when it officially formed itself into the St. Francis of Assisi Mission Congregation.  The first Vicar for the St. Francis congregation was the Reverend James Murray. A native of Charleston, South Carolina, Father Murray had attended Morehouse College, Atlanta, Georgia, and Bishop Baines Seminary in Virginia.  Although he was Vicar of St. Francis, Father Murray continued to serve as Vicar of St. James’ Episcopal Church in Austin, Texas, a ministry he had begun in the late 1940's.

Other early leaders in the establishment and development of the church included Dr. E. B. Evans, who served as president of Prairie View A. & M. College from 1946-1966, Mr. and Mrs. R. B. Atwood, Bishop Denby of Cleveland, Ohio; and Father John B. Boyce, Mrs. Ann C. Preston, Colonel West A. Hamilton, the Menke family of Hempstead, Mrs. Eula Dooley, Mrs. Jimmie Ruth Phillips, Dr. and Mrs. C. H. Nichols, Mrs. Eloise Williams, Dr. J. L. Brown, Mrs. Naomi Thomas Baker, Mr. John Ledbetter, Dr. & Mrs. R. Von Charleton, Dr. & Mrs. E. G. High, Dr. & Mrs. D. S. Yarbrough, Mr. & Mrs. Julius Jones, Ms. Kathryn Jordan, Ms. Nerissa Stickney, Mrs. Ollie Mae Scott, Mr. & Mrs. William E. Reid, Sr. and Mr. H. E. Mazyck, Jr.

On June 16, 1957, the Reverend Charles F. Hood relieved Father Murray as Vicar and served the congregation until December 31, 1959. Up to t he administration of Father Hood, the St. Francis’s congregation had met in the Guest House Building on the campus of Prairie View.

On June 15, 1958, the former church building of St. Bartholomew’s Episcopal congregation, Hempstead, having been moved to Prairie View, began to serve as the church building for the St. Francis congregation. This building, erected in 1870 and one of the oldest frame Episcopal churches in the Diocese of Texas, is now one of the three remaining churches consecrated by the Rt. Reverend Alexander Gregg, the first Bishop of Texas. At a special service in the evening of May 16, 1963, the Waller County Historical Society with the assistance of the Army ROTC of the College erected a Texas Historical Society plaque in the vestibule of the historic church. Since 1994, the building now serves as the home for Hope AME Church in Prairie View, Texas.

With a church building of their own, the St. Francis congregation was able to conduct the full ritual of the Episcopal Church. The opening day services of the church building saw the baptisms of Dannis ‘Frontious’ Michael Ledbetter. On the Feast of St. James the Apostle, July 25, 1957, the Rt. Reverend Frederick Percy of Goddard, Suffragan Bishop of the Episcopal Diocese of Texas, conferred the Rite of Confirmation for the first time within the congregation on nine candidates St. Francis of Assisi Episcopal Church. The first Marriage Rite for the congregation took place between Mr. George Murrel Sims and Miss Nell Rose Antoine on May 12, 1961. The Reverend Hugh Donald Keeling succeeded Father Hood as Vicar on January 1, 1960 and served the congregation until his transfer to St. Mary’s Episcopal Church, Belleville, Texas on January 15, 1963. Father Keeling’s successor as Vicar was the Reverend James T. Moore, who served the congregation until 1968.

On October 4, 1964, the congregation inaugurated the annual custom of celebrating the patron feast of the mission, the Feast of St. Francis of Assisi, with a Solemn High Eucharist followed by a procession with the Saint’s stature through the streets of Prairie View and concluding with a parish supper. The congregation marked the assassinations of President John F. Kennedy and Dr. Martin Luther King, Jr., with appropriate Requiem services.  On October 10, 1969, the Rt. Reverend Josiah Mtekateka, Bishop of Lake Malawi, Africa, pontificated a Solemn Even Song Service.  Earlier in the day the bishop had addressed a campus-wide luncheon in the Memorial Student Union. 

A particularly happy occasion for the congregation was on June 15, 1969 when the first Vicar, Father James Murray, since attached to the Houston Metropolitan Ministries and Incarnation Episcopal Church, Houston, Texas, returned to St. Francis to celebrate the twenty-fifth anniversary of his ordination as a priest.