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 currently no family housing on board this station.)

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.