Joint Base Myer-Henderson Hall is the result of a merger of three bases, two Army forts and one Marine Corps facility.

The oldest part of JBMHH is the McNair military reservation, which has been in service for over two centuries. It was established in 1791 as the Washington Arsenal, and renamed after Lieutenant General Lesley McNair in 1948. It was originally established to protect the new city of Washington. When the British invaded in 1814, the arsenal was overwhelmed, overrun, and burned, after the quick removal of powder and mobile equipment, and destruction of immobile equipment.

The Arsenal was rebuilt in the years after. In 1826 the post saw the construction of the first U.S federal penitentiary. This is where, following the Civil War, the conspirators of Lincoln's assassination were tried, found guilty, and hanged. The arsenal was closed in 1881, and transferred to the Quartermaster Corps. During this time, Major Walter Reed, an Army doctor, used the area's marshlands as a site for his research on malaria. As a result, his work helped discover the cause of yellow fever.

During the early 1900's, more changes took place, with most of the post rebuilt. The post became home to the National War College in 1901; and shortly after, the Industrial College of the Armed Forces was established here in 1924. It quickly built a reputation for study of industrial mobilization, as well as a prepping program for officers training to work in high level posts in Army supply organizations. As a mainly training post, most of the rest of Fort McNair's history was quiet, until 1966, when McNair became headquarters for the US Army's Military District of Washington. In 1976, the War College and Industrial College combined to become the National Defense University.

As a result of the BRAC of 2005, Fort McNair joined Fort Myer and Henderson Hall as a joint base. It is the home of the U.S Army Military District of Washington, the Inter-American Defense College, the National Defense University, the US Army Center of Military History, and the 3rd U.S Infantry Regiment.

The Meyer side of Joint Base Myer-Henderson Hall dates back to the Civil War. The land of the fort was originally owned by the grandson of Martha Washington, George Washington Parke Custis, which had come into public possession. Some of the land was designated as Fort Whipple, and in 1881, the fort was renamed Fort Myer, after General Albert J. Myer, surgeon and "Father of the Signal Corps".

In the late 1860's, the fort was designated as the nation's cavalry showplace, and used as the headquarters of the Signal Corps, because its high elevation made it great for visual communications. In the early 1900's, the fort was the site of the first military test flight. Orville Wright demonstrated the airplane for military observation at Myer in 1908. The plane successfully stayed in the air for one minute and eleven seconds. The second test flight lasted for four minutes before crashing, killing his passenger, Lieutenant Thomas Selfridge. Selfridge's death was the first powered-aviation fatality; Orville Wright survived with minor injuries.

During WWI, the fort served as a staging area for engineering, artillery, and chemical companies and regiments, while in WWII, the fort was a processing station for soldiers entering and leaving the Army. Also during that period, the Army's elite ceremonial units the U.S Army School of Music, the U.S Army Band, and the U.S Army Chorus relocated to the post in 1942. Presently, as an outcome of the 2005 BRAC, Fort Myer combined with the Marine Corps' Henderson Hall to become the first Joint Base in the Department of Defense, forming Joint Base Myer-Henderson Hall.

Henderson Hall was established in 1942 as a headquarters building for the USMC, allowing relocation of certain commands out of the Navy Annex. Many of the Marines on board Henderson Hall during the war were (as they were called at the time) Woman Marine Reservists, enrolled to perform clerical duties. Henderson Hall had a woman's barracks during World War Two, allowing easier housing for the Reservists in crowded Arlington. (There is no family housing on board this station, as of 2013.)

Henderson Hall is named for Commandant Archibald Henderson, the longest serving commandant of the Marine Corps, in that position for 38 years of a 53 year career.
Henderson Hall was joined with two other military bases, Fort Myer and Fort McNair, in the 2000s, as part of base realignment.