[4] When the Civil War began, the Commonwealth of Virginia seceded from the United States, Lee resigned his commission, and he and his wife left the estate.

The United States Government then confiscated the estate and began to use it as a burial ground for Union Army dead (see Arlington National Cemetery), to house freed slaves (Freedmen's Village),[5] and for military purposes, including the Civil War defenses of Washington (see Washington, D.C., in the American Civil War).

The Army named the fort after Brevet Major General Amiel Weeks Whipple, who died in May 1863 of wounds received during the Battle of Chancellorsville.

Fort Whipple, with its fortifications abandoned, then became the home of the Signal School of Instruction for Army and Navy Officers, established in 1869.

On 17 September 1908 it became the location of the first airplane fatality, as Lt. Thomas Selfridge was killed when on a demonstration flight with Orville, at an altitude of about 100 feet (30 m), a propeller split, sending the aircraft out of control.

The United States Navy established the nation's first radio telecommunications station, NAA, near Fort Myer in 1913.

In 1915, the station's radio towers, "The Three Sisters", transmitted to Paris the first wireless communication that crossed the Atlantic Ocean.

[16] During World War I, Fort Myer was a staging area for a large number of engineering, artillery, and chemical companies and regiments.

The area of Fort Myer now occupied by Andrew Rader Health Clinic and the Commissary were made into a trench-system training grounds where French officers taught the Americans about trench warfare.

General George S. Patton Jr., who was posted at Fort Myer four different times, started the charitable "Society Circus" after World War I.

[21] The fort was designated a National Historic Landmark in 1972, for its well-preserved concentration of cavalry facilities and officers' quarters, and for its importance in military aviation history.

[23] The book, Images of America: Fort Myer, contains a copy of a handwritten letter from Abraham Lincoln that appointed General Whipple's oldest son to the United States Military Academy at West Point.