The mission of the MEU is to provide geographic combatant commanders with a forward-deployed, rapid-response force capable of conducting conventional amphibious and selected maritime special operations at night or under adverse weather conditions from the sea, by surface and/or by air while under communications and electronics restrictions.

It is one of three West Coast MEUs which make periodic deployments to the Western Pacific, Indian Ocean and Persian Gulf regions.

[9] In mid-13 November MEU (SOC) became the principle rapid response force in the region and executed two humanitarian assistance operations.

During this period the MEU conducted a Maritime Interdiction Operation/Visit Board Search and Seizure (MIO/VBSS) mission aboard the Honduran-flagged merchant vessel Ajmer, which was in violation of United Nations sanctions on Iraq.

[10] In January 1995, the 13th MEU (SOC) was ordered to conduct Operation United Shield - the withdrawal of UNOSOM forces from Somalia.

On 28 February, the 13th MEU (SOC) conducted an amphibious assault onto Somali soil and executed a relief-in-place with UNOSOM forces.

In October 2000, the 13th MEU was dispatched to provide security and assist in Operation Determined Response, the recovery of the crippled destroyer USS Cole in the port of Aden, Yemen.

The MEU marked its transit home with a stop on Iwo Jima, and Tarawa, returning to Camp Pendleton 13 February 2001.

The "Fighting 13th’s" thirteenth deployment began six weeks early when it departed 1 December 2001, in response to Operation Enduring Freedom being conducted in Afghanistan.

The MEU conducted separate bilateral training exercises with Qatari and Omani forces prior to returning to Camp Pendleton 17 June 2002.

[14][15][16] On 16 June 2016, AV-8B II+ Harriers of the 13th MEU flying from the USS Boxer in the Persian Gulf began airstrikes on ISIL in Iraq and Syria as part of Operation Inherent Resolve.