US Navy presence in Key West goes back to 1822, the year Florida became a US Territory. In March 1822 Lt. Cmdr. Matthew C. Perry physically claimed the Florida Keys by planting a US flag on Key West. Lt. Cmdr. Perry went on to a nearly 50 year career in Navy service, as the father of the "Steam Navy" and later, as Commodore (a rank roughly between Captain and Rear Admiral) in command of the 1852-1854 US mission to open Japan to trade.

Key West held a commanding position for the Gulf of Mexico and Caribbean Sea, which naturally invited a shore base, and in 1823 a Navy base was established under command of Commodore David Porter. The base supported a Navy "Mosquito Fleet" with a mission of suppressing local piracy, still a serious threat in the area at that time. In the following decades the Navy also suppressed slave shipping, illegal after 1808, and enforced customs law. In the Civil War the Navy base kept Key West in Union hands, and was the base for interdicting blockade runners to Confederate shores. In 1898 the USS Maine sailed from Key West Naval Base, where it sank, leading to the Spanish-American War, which led to to US possession of several former Spanish overseas territories.

The aviation history of Key West starts in 1917, when the Navy established a basic air station with three seaplane ramps, a dirigible hangar, a hydrogenerator plant (to make hydrogen gas for the blimps), and temporary barracks housing, all for aviation training in the steadily good flying weather of the Keys. A submarine base was also established, and the dirigible and seaplanes were intended for anti-submarine patrolling. They never found any, but this was the birth of US Navy anti-submarine warfare. Some 500 Naval aviators were trained at Key West, but the close of the war led to the relocation of most aviation station and sub base assets, with only a radio station left operating. The main Key West Navy base was also greatly reduced in operations.

In 1939, with world-wide war breaking out, Navy Base Key West was revived as a station for destroyers, submarines, surface patrol craft, and patrol seaplanes, with additional fields established for carrier aircraft and patrol blimps. This time, the value of the anti-sub patrols was clear: German U-Boats were torpedoing Allied shipping within sight of US shores, with a peak of 49 ships sunk in May 1943.

The end of the war led to the closing of the Naval station, but the air station remained active, with all fields combined under NAS Key West, primarily as a training center. The location of NAS Key West proved its value in 1961, with the sudden development of the Cuban Missile Crisis - this was the closest US military installation to Cuba at the time other than Guantanamo Bay Naval Base.

In the 1990s NAS Key West supported Operation Support Democracy, in Haiti, and since the 1980s has supported anti-drug smuggling operations in conjunction with the US Coast Guard and other Federal agencies.