Before World War Two the Department of War (the previous name of the Department of the Army) and the Department of the Navy were completely separate, in their own buildings. They had different missions, did not need to interact much, and did not need to coordinate. Furthermore, the War and Navy Departments were spread out from their own Bureaus and generally crowded. World War Two changed that, and with the arming programs of the late 1930s and early 1940s it was recognized that both departments needed to be headquartered at high levels near each other, or better yet in the same building.

In May 1941 the plan for a new War Department building progressed. A plan was drawn up for the new building to be located at Arlington Farms, an irregular shape requiring a bent pentagon building. The site actually chosen was the local slum, Hell's Bottom, which was not a strange shape, but the basic pentagon shape was kept, to save redesign costs, and turned into a regular Pentagon. President Franklin D. Roosevelt backed the plan and Congress voted funding; foundation clearance began September of 1941. Hell's Bottom was cleared, including local factories, warehouses, pawn shops, bars, "seedy locations," and private housing. This took only several weeks and foundation was soon laid. Steel was in short supply, with arming and ship building taking up most of production, so the bulk of the building was made out of reinforced concrete. Construction was rapid, due to the pressure of the sudden outbreak of war and aggressive target dates; the first new tenants moved into their new offices while construction was still underway in the next wing.

Construction was complete in only 16 months, and became the US center of the war effort immediately. In 1949 the Dept. of War was dissolved, and the Army, Navy, and Air Force were all placed under the Department of Defense, headquartered at the Pentagon. The Secretaries of Defense, the Army, Navy, and Air Force, the Joint Chiefs of Staff, several vital security agencies, and DARPA are all headquartered here. Over the decades the Pentagon has been the site of several public protests, and on September 11 2001 was the target of a terrorist attack, which happened to hit during a reconstruction and restrengthening phase. The damage was repaired and since then the entire building has been reinforced.

From the very beginning was a small city in its own right. The Pentagon has been the largest office building in the world since opening, and has its own police force, protection agency, six zip codes, a food court with over twenty food vendors, a fitness center, and an exchange. It is not a base, however, and has no on-site housing. Today, roughly 28,000 personnel work at the Pentagon. Despite its size, it is possible to walk from one far point end to the other midpoint in less than ten minutes. The building also has double the restroom facilities it should for a building this size, due to segregation rules at the time, which were immediately discarded by President Roosevelt. Until 1965, the Pentagon was the only building in Virginia with no segregation.