Dorothy Rust and Lavinia Hamilton founded the school in 1928 as the Warrenton Branch of the Calvert School of Baltimore.

There were nine students in the original School, which met in the basement of the John Barton Payne Building in Old Town Warrenton. In 1929, the School relocated to the St. James Episcopal Church parish house, where it remained until 1942. After a year in Mrs. Rust's home, the School moved to a converted stable on Green Street , where it remained until the mid 1950's.

At the urging of alumni, in 1957 Mrs. Rust created a large and modern home for the School in its current location. At the same time, she changed the name of the School to Highland School. In 1958, Mrs. Rust sold the School to the non-profit Fauquier Educational Foundation run by an independent Board of Trustees.

In 1989, the current organization of the School was established. The School was incorporated as Highland School, Incorporated. A new Board of Trustees was established, with 16 members selected from parents, alumni and the community.

The physical structure of the School also evolved. In 1964, the first addition to the original building added a classroom. The Chilton Building, which currently houses PK and Kindergarten, was built in 1968. In 1979, three new classrooms were added and the library was expanded. A new gym was built in 1985, and as part of this project a new facade and larger office spaces were incorporated.

IIn 1993, the school's Board of Directors undertook the creation of a detailed master plan for the School's future. It was decided that the School be expanded to improve diversity and to allow for a substantial investment in state of the art musical, artistic, and scientific facilities. In the summer of 1994, the School's grounds were expanded by the donation of twenty-two acres of land adjoining the original site.

The first part of the master plan was to expand each grade from one section to two at the start of the 1995-1996 school year, and this entailed a major renovation and expansion in the spring and summer of 1995. New science labs were added for both the Lower School and the Middle School. Ten classrooms were added. A new art center, music room, computer lab, guidance center, resource room, and an expanded library were also part of this improvement, in which the Lower School took on its current shape of 71,000 square feet.

Next in the plan was the establishment of an Upper School. Phase I of the Upper School plan was completed over the summer of 1996, and the Upper School opened that fall with eleven classrooms and a gymnasium. Phase II, which added an additional ten classrooms, a library, and office space, was completed in 2001. Phase III, which added five classrooms and a three hundred seat auditorium, was completed in 2004 and marked the successful conclusion of the first ten-year Master plan.