In the early 1700s when the ships from England were scouting the coastline looking for likely places to settle, they were plagued by attacks from pirates.  In desperation they searched for a place to moor the ships in safety.  Soon a passage was discovered through the difficult New River inlet and a small bay found that allowed protection for several ships at a time.  As more ships commuted, it was evident that records must be kept and protected. However, the ship's logs were becoming more of a burden to the ship's company.  In 1731, a working party was organized among the settlers to go ashore and erect a cabin, later called the Courthouse, to store their important documents.  This was accomplished, thus, the area surrounding the Courthouse became known as Courthouse Bay.  

Today, Courthouse Bay is the home of Marine Corps Engineer School, 2d Assault Amphibian Battalion, 2d Combat Engineer Battalion, 2d Reconnaissance Battalion, 2d Marine Raider Battalion, and United States Coast Guard Special Missions Training Center.

The first Engineer School in the Marine Corps was activated at Quantico, Virginia, as part of the Training Center on 8 May 1941.  A four-course curriculum consisted of Refrigeration, Water Distillation and Purification, Demolition, and Camouflaging.

In August 1942, the Engineer School moved to the newly organized Training Center, Fleet Marine Force, Marine Barracks, New River, North Carolina.  The following courses were added to the original curriculum: Basic Surveying, Bridging, Drafting, Aerial Photographic Interpretation, Field Electrician, Map Reproduction and Photography (was retitled Photo-Lithography), Shop, Engineer Equipment, Water Supply, and Well Drilling.  The Engineer School was detached from Marine Barracks, New River (redesignated Camp Lejeune) and reorganized into the Engineer Battalion, Training Center, Camp Lejeune, North Carolina on 31 December 1942.

The first officer’s course began on 5 October 1943.  A Specialist Training Regiment was organized on 14 July 1944 which included the Engineer Battalion.  The Engineer School Battalion continued to be part of the Regiment until July 1946.

On 31 July 1947, the Engineer School Battalion was disbanded.  The school was once again activated on 1 January 1949 and designated Engineer School Company, Headquarters and Service Battalion, Marine Barracks, Camp Lejeune, North Carolina.  Between January 1949 and November 1950, Engineer School Company was redesignated Engineer School Battalion, and relocated to its present base of operations at Courthouse Bay, Camp Lejeune, North Carolina.

A suitable name for the school was finally arrived at in April 1952, when the school was renamed The Marine Corps Engineer School, Marine Corps Base, Camp Lejeune, North Carolina.

During November 1976, Marine Corps Engineer School began a complete reorganization.  The Student Command was deactivated and personnel were distributed to provide appropriate manning levels for four separate companies - Headquarters and Service Company, Engineer Equipment Instruction Company, Utilities Instruction Company, and Combat Engineer Instruction Company.  Reorganization was completed and full operation began on 3 January 1977.

In 1995 the Engineer Equipment Instruction Company was relocated to Fort Leonard Wood, Missouri as part of the Inter-service Training Review Organization.

Between 2004 and 2014 Marine Corps Engineer School underwent several changes to its organization.  The end result increased the span of responsibility for the schoolhouse to include involvement in Engineer Training & Education, Doctrine, and Capability Requirements development.  These additional responsibilities demand increased interaction with the Operating Force and close coordination with the Engineer Advocate at HQMC Installations & Logistics.  Additionally, Marine Corps Engineer School has been assigned as the Marine Corps proponent for Counter-Improvised Explosive Device (C-IED) Defeat the Device training and has been providing this training to Marines since 2007.

The Marine Corps Engineer School started in 1941 by providing four courses and now MCES provides instruction in 21 different programs of instruction in both the basic combat engineer and utilities engineer skill sets training approximately 2,000 Marines each year. Additionally, as the USMC proponent for C-IED and Defeat the Device training MCES provides training to approximately 50,000 personnel annually in pre-deployment Counter-Improvised Explosive Device training in 6 different Counter-Improvised Explosive Device Programs of Instruction.