The squadron saw frequent action in the Pacific theater during World War II before being decommissioned on 30 November 1945.

During September 1966, the squadron deployed to Chu Lai Air Base, Republic of Vietnam and remained until October 1970.

H&MS-13 used first the Grumman TF-9J Cougars and later Douglas TA-4F Skyhawks as fast forward air control aircraft in support of ground troops.

On 15 January 2003, Marine Aviation Logistics Squadron 13 embarked 205 Marines and equipment aboard the USS Bonhomme Richard in support of combat operations in Southwest Asia, deploying detachments ashore with MALS-13 Forward during Operation Southern Watch and Operation 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 and returned to MCAS Yuma.