The facility was established initially by the United States Navy as a Naval Training Station (USNTS Sampson) in 1942.

The Navy obtained 2,600 acres of former farmland and also vineyards for the facility on the east side of Seneca Lake, New York.

In 1949, the former naval station was turned over to the United States Department of Agriculture, which used the buildings as warehouses and granaries.

With the outbreak of the Korean War, the United States Air Force took interest in the former Naval Station for use as a Basic Military Training (BMT) Base.

The mission of Sampson AFB was to provide formal basic training for all male and female enlisted personnel not having sufficient previous military training; to establish and operate such assembly, processing and separation station as specifically directed; to provide a comprehensive counseling program for Basic Indoctrinee personnel in order that these airmen may be most effectively assigned in accordance with Air Force requirements; and to maintain training programs for accomplishing rehabilitation of garrison prisoners.

With the opening of Sampson and Parks AFB for BMT, Shortly thereafter, ATC increased basic military training from seven weeks to eight.

In July 1952 the Air Staff approved a 12-week course, which ATC implemented on 1 August at Lackland and Parks and on 1 September at Sampson.

However, after only two months, the Air Staff decided that the course should be shortened, and ATC developed an 11-week program to begin in January 1953.

By the time it was closed, over 300,000 airmen received basic training at Sampson AFB in preparation for service in the Korean War, as well as service in USAFE, Far East Air Force, and other United States Air Force major commands both in the United States and around the world.

In 1971, the State of New York closed the School due to budget cuts and while empty, a fire destroyed most of the main hospital complex.

Air Force C-123 and C-130 cargo aircraft also used the runway on occasion for transporting personnel and material to the depot.

The main gate on Sampson State Park Road, west of the intersection with NY Highway 96A 42°43′45″N 76°53′35″W / 42.72917°N 76.89306°W / 42.72917; -76.89306, still stands guard over the base.

This article incorporates public domain material from the Air Force Historical Research Agency