Provisional Headquarters and Maintenance Squadron 39 was activated on 16 April 1968 at Marine Quang Tri Airfield, Republic of Vietnam.

Assigned to Provisional Marine Aircraft Group 39 (MAG-39) of the 1st Marine Aircraft Wing, the squadron's mission was to provide logistical support for the tactical squadrons and tactical elements located at Quang Tri, Dong Ha, and Khe Sanh.

Headquarters and Maintenance Squadron 39 was reactivated at Camp Pendleton, California on 1 September 1978 to provide support for the UH-1 "Huey", AH-1 "Cobra", and OV-10 "Bronco".

This changed placed aviation logistics support function firmly under the cognizance of one commanding officer to more efficiently and effectively serve the requirements of supported flying squadrons and Marine Air-ground Task Forces.

MALS-39 provides all the aviation supply and intermediated level of aircraft maintenance, avionics, and ordnance support for nine flying squadrons.