In 1941 only a dirt airstrip existed. At this time a request by the City of Gainesville was placed with the Civil Aeronautics Administration of the United States for a municipal Airport.
In 1943 the U.S. Navy leased the airport land from the City of Gainesville for one dollar to be used by the military during World War II. At that time the Navy had sufficient land to permit development of the intersecting 4,000-foot paved runways with parallel taxiways, aircraft and electronics maintenance facilities, barracks and related support facilities.
The base functioned as a satellite of the Naval Air Station at what is now Dekalb-Peachtree Airport. The mission of the Gainesville facility was to train ground personnel in ground-controlled approach (GCA) procedures.
Truck-mounted radar was used to track approaching target aircraft. Some of the equipment that was in use at the time can be seen in the black and white photographs in the main terminal building. Some of the buildings that were used can be identified as the terminal and control tower (tower not used since WW II), large radar maintenance hangar, Navy brig, and an aircraft maintenance hangar that still exists today.
In 1947 the facility was decommissioned and returned to the City of Gainesville. In addition to the improvements to the land and runways, all building and equipment became the property of the City of Gainesville.
Over the course of the next 35+ years, from 1964 to the present day, numerous improvements have been made. These have been funded from such sources as the FAA, State of Georgia, Appalachia Fund, General Government Funds, and the City of Gainesville totaling over $4.3 million dollars. These improvements have ranged from relocating beacons, marking the runways and the construction of a parallel taxiway in 1979, to the strengthening and extending of the runways and all of the navigational devices.
In 1971 the airport was named in honor of local aviation pioneer Lee Gilmer who owned and operated Gilmer Flying Services before, during, and after WWII.