The early history of Linton Hall has its roots in the donation of land by Sister Baptista Linton for the education of poor boys and girls. The Benedictine Fathers established St. Maurus Boys' School in 1893; the Benedictine Sisters established St. Edith's Academy for girls in 1894.

After World War I, the enrollment of both schools began to decline. The Benedictine Fathers returned to their abbey in Belmont, North Carolina. In 1922, the Benedictine Sisters started two schools: St. Gertrude High School for girls in Richmond, Virginia, and Linton Hall School, a residential school for boys in Bristow.

Linton Hall began as a military school; however, the military program was discontinued for a few years. In 1932,  the military program was firmly established, and the school became known as Linton Hall Military School. As the enrollment increased, the monastery building lacked adequate space for housing the academic and residential programs. In 1940, two floors of St. Ann's Guest House were converted into dorms.  In 1946, the first phase of the present building was completed and served as a residence hall for all the students. By 1951, the second and third floors and the classroom wing were completed. Physical education facilities included a gymnasium built in 1956, an outdoor swimming pool constructed in 1968, tennis courts, a primary grades Welker Memorial playground, various playing fields, and a playground purchased by the Parent School Guild.