The 99th Trooper Carrier Squadron was activated on August 1, 1943 at Sedalia Field Army Airfield in Missouri. The squadron's first combat mission was to drop members of the 101st Airborne Division into France as part of the June 6, 1944 assault on Normandy. During World War II the squadron operated C-47 planes and CG-4 gliders.

The Squadron was redesignated the 99th Trooper Carrier Squadron, Medium on May 10, 1949. On December 27, 1965 the squadron was redesignated the 99th Military Airlift Squadron, Special Mission. On September 12, 1977 the squadron was redesignated the 99th Military Airlift Squadron. Finally, on July 12, 1991 the squadron was redesignated as the 99th Airlift Squadron.

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