Founded by the Sisters of St. Joseph, St. Francis Xavier School began as St. Joseph's School which was established in Brunswick in 1900. Reverend P.J. Luckie, S.M., requested that Rt. Reverend Benjamin J. Keiley, D.D., Bishop of Savannah, start a Catholic school in St. Francis Xavier parish. The Sisters of St. Joseph started and staffed the school in September of that same year.

A former boarding house on the corner of Richmond and Howe Streets became the first school opening with 60 pupils. Even in the beginning, this number of pupils proved to be too many for the building to accommodate, so in the spring of 1902, property was purchased and work begun on the colonial type building which served as convent and school for so many years.

In 1953 a new convent, designed by C.M. McGarvey, was built for the sisters. In 1955 plans were begun by Reverend James Cummings, S.M. for the erection of a new school. The new name, St. Francis Xavier School, replaced St. Joseph School as a tribute to the people of the parish who generously supported a parochial school.

The new building, located at 1121 Union Street directly east of the Church property, originally consisted of eight classrooms and a Kindergarten, a cafetorium and kitchen, a library and book supply room, lavatories, Principal's office, health room and teacher's lounge. The main building was built surrounding a lovely courtyard. Two new classrooms were built in 1964. Since then further expansions include a building for Kindergarten, a building for the Pre-School and Parish Center which is shared by the parish and school.

The mission of the Sisters of St. Joseph continues to be carried out at St. Francis Xavier School by Miss Erin Mary Finn, principal, Sister Anna B. Kearns, CSJ, and a dedicated faculty and staff.