Construction of Fort Stanton began in September 1861 to defend the Navy Yard. By October 22, the fort was completed and platforms were laid for ten 32-pounders, though none of the guns had been received. Fort Stanton's perimeter of 322 yards was to be armed with 18 guns. A garrison of 483 men would man the fort.
By February 1862, the fort was fully gunned and garrisoned by companies of the 4th New York Heavy Artillery Regiment and the 88th Pennsylvania Infantry.
On June 23, 1865, General Order 89, listed Fort Stanton as a second level fortification and need for defense of the city. By July however, Fort Stanton was abandoned and material within it sold to the highest bidder.
Fort Stanton was named in honor of Secretary of War Edwin Stanton. Stanton resigned from this position in May 1868, and returned to his private practice as a lawyer. His wish to sit on the Supreme Court appeared to be fulfilled when President Grant appointed him, and the Senate confirmed him on the same day, December 20, 1868. He died four days later in Washington, D.C.