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 First 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. Provisional Headquarters and Maintenance Squadron 39 was deactivated on 25 October 1969.
Headquarters and Maintenance Squadron 39 was reactivated at Camp Pendleton, California on 1 September 1978 to provide support for the UH1 "Huey", AH1 "Cobra", and OV-10 "Bronco". The squadron was redesignated on 1 October 1988 as Marine Aviation Logistics Squadron 39 (MALS-39). 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. Additionally, whenever the flying squadrons deploy, whether in the United States or overseas, MALS-39 augments these squadrons with its Marines to ensure optimum aviation logistics support in every clime and place.
During the last ten years, Marines from MALS-39 have seen action throughout the world. Elements of the squadron participated during the Gulf War and in the liberation of Kuwait. Magicians also participated in Operation RESTORE HOPE in Somolia Africa, and in January 2003, the squadron deployed as a command in support of Operation ENDURING FREEDOM and Operation IRAQI FREEDOM both aboard the SS CURTISS Aviation Logistics Support Ship, and ashore at Ali Al Salem Kuwait and at various Forward Operating Bases throughout Iraq. In February of 2004, Magicians deployed as logistician augments to Marine Aviation Logistics Squadron 16, and as force protection augments to 3d Low Altitude Air Defense Battalion in support of Operation IRAQI FREEDOM II. MALS-39 Marines continually deploy to the Western Pacific supporting unit deployments to Okinawa, Japan and Marine Expeditionary Units afloat. Routinely, the Squadron provides personnel, equipment, and aviation components in support of Combined Arms Exercises at Marine Corps Air/Ground Combat Center, 29 Palms, CA, Weapons and Tactics Instructor Courses at MCAS Yuma, AZ, and Desert Talon Exercises at MCAS Yuma, AZ.
MALS-39 has received numerous honors and decorations which include: Presidential Unit Citation Streamer, Navy Unit Commendation Streamer, Meritorious Unit Commendation Streamer with one Bronze Star, National Defense Streamer with one Bronze Star, Vietnam Service Streamer with one Silver Star, Vietnam Cross of Gallantry with Palm, and Vietnam Meritorious Unit Citation Civil Action Streamer. The Squadron has been recognized also for its logistics accomplishments, winning the 1998 Secretary of Defense Maintenance Award (Medium Category) and the 2003 Marine Corps Aviation Association Marine Aviation Logistics Squadron of the Year.