JB Charleston was created in 2010 from a merger of Charleston Air Force Base and Naval Weapon Station Charleston.

Charleston Field began as Charleston Municipal Airport, in 1928 a local effort to make sure the city of Charleston had a hand in the blockbuster new technology of the time, air travel. The city, with Federal assistance, kept the airport up to date through the 1930s, as part of a military preparedness program. In 1941, after the attack on Pearl Harbor Charleston Airport was placed under control of the Army Air Force, on lease, and two pursuit groups were relocated to the newly redesignated Charleston Army Air Base. This was shortly followed by the relocation of three observer squadrons, and soon an antisubmarine bombing squadron. Naturally, this sudden transfer of units to a civilian facility had not allowed for proper construction of barracks housing, administration, or recreation facilities, and the airport was still being used for limited civilian flights. This was a cramped time at Charleston. The base was expanded in size, and many of the air units were deployed overseas within a year; the war effort had shifted, and Charleston AAB was redesignated Charleston Army Air Field in 1943. The AAF was used for bomber crew training, in addition to ongoing anti-sub patrols.

After the war, Charleston AAF was declared surplus, and returned to civilian control. This lasted until the Cold War prompted a rearming wave, and the airport entered a joint military-civilian use lease, splitting operations between Charleston Airport and Charleston Air Force Base. Given the civilian presence, the base focused mainly on troop airlift, with an interceptor/escort mission. After the end of the Cold War, base and force shifts prompted a merger with NWS Charleston.

Naval Support Activity Charleston, formerly a Naval Weapon Station, was commissioned November 1941, one month before the attack on Pearl Harbor. The activity of the weapon station (then the US Naval Ammunition Depot) was to store ammunition and load it onto ships produced at the now closed Charleston Naval Yard. After the war, the Depot removed munitions from ships, and then dropped to a low activity status for several years. In the 1950s and 1960s the Depot oversaw not only conventional munitions support, but also nuclear arms loaded onto ballistic submarines. This mission continues, with several conventional and nuclear munitions missions, including the Naval Nuclear Power Training Command, explosives fusing and defusing training, the Space and Naval Warfare Systems Center, a Coast Guard station, Border Patrol academy, and multiple logistics centers. This has required multiple expansions of station facilities over the years, including various engineering buildings, storehouses, and on base housing units, and recently a large medical center.

In 2009 the two Charleston military bases were merged (conveniently with the same name), following a general refurbishment, particularly of the field runways.