Marine Aviation Logistics Squadron 13 was activated on 1 March 1942, at San Diego, California, as Headquarters and Service Squadron 13. The squadron saw frequent action in the Pacific theater during World War II before being deactivated on 30 November 1945. The squadron was reactivated 15 March 1951, at El Toro, California, as Headquarters and Maintenance Squadron 13, Marine Aircraft Group 13, Air fleet Marine Force, Pacific. After several West Pac deployments and relocations, the squadron was reassigned during April 1966 to the 9th Marine Amphibious Brigade, Fleet Marine Forces Pacific. During September 1966, it deployed to the Republic of Vietnam.
The squadron participated in the Vietnam conflict from 1966 to October 1970. The squadron was then relocated to El Toro, California, and assigned to the 3d Marine Aircraft Wing until 1 October 1987, when the squadron moved to MCAS Yuma. On 5 October 1988, the Headquarters and Maintenance Squadron within the Marine Aircraft Group (MAG) was replaced by the creation of the Marine Aviation Logistics Squadron (MALS).
During the period of 10 August 1990 to October 1991, Marines from Marine Aviation Logistics Squadron 13 responded expeditiously in providing aviation logistics support for subordinate units within Marine Aircraft Group 13, 3d Marine Aircraft Wing, and I Marine Expeditionary Force, Aviation Combat Element (ACE) activities during operations "Desert Shield and Desert Storm." After successful combat operations against enemy forces in operation "Desert Storm," MALS-13 personnel continued to be deployed to the Arabian Gulf region to augment Commander, Marine Forces, Southwest Asia Security Forces and assist in the reconstitution of the Maritime Prepositioning Forces ships.
In October 2002, the Squadron was tasked with providing a Remote Expeditionary Support Package (RESP) to support six AV-8B aircraft in combat operations in Afghanistan during Operation Enduring Freedom. This was the first employment of the RESP since its conception. This detachment of MALS-13 personnel returned October 2003.
On 15 January 2003, Marine Aviation Logistics Squadron 13 embarked 205 Marines and equipment aboard the USS Bonhomme Richard LHD-6 in support of combat operations in Southwest Asia, deploying detachments ashore with MALS-13 Forward during Operations Southern Watch and Iraqi Freedom at Al Jaber Air Base, Kuwait and An Numiniyah Expeditionary Air Field, Iraq.
In May 2003, Marine Aviation Logistics Squadron 13 disembarked USS Bonhomme Richard LHD-6 into Al Jaber Air Base, Kuwait and returned to MCAS Yuma.
During its distinguished history, Marine Aviation Logistics Squadron 13 had been awarded the Presidential Unit Citation Streamer with one bronze star, Navy Unit Commendation Streamer with four bronze stars, Meritorious Unit commendation Streamer with two bronze stars, Asiatic-Pacific Campaign Streamer with one bronze star, WWII Victory Streamer, National Defense Service Streamer with two bronze stars, Armed Forces Expeditionary Streamer, Vietnam Meritorious Unit Citation with two silver and one bronze star, Vietnam Cross of Gallantry with Palm Streamer, Vietnam Meritorious Unit Citation with Civil Actions Streamer, Southwest Asia Service Streamer with two bronze stars, and the Global War on Terrorism Expeditionary Streamer.