The fort is named for Revolutionary War hero Dr. Joseph Warren, who sent Paul Revere on his famous ride, and was later killed at the Battle of Bunker Hill.

Fort Warren was built from 1833 to 1861 and was completed shortly after the beginning of the American Civil War as part of the third system of US fortifications.

The Army engineer in charge during the bulk of the fort's construction was Colonel Sylvanus Thayer, who is best known for his tenure as Superintendent of the United States Military Academy at West Point, New York.

James M. Mason and John Slidell, the Confederate diplomats seized in the Trent affair, were among those held at the fort.

Confederate military officers held at Fort Warren included Richard S. Ewell, Isaac R. Trimble, John Gregg, Adam "Stovepipe" Johnson, Simon Bolivar Buckner Sr., and Lloyd Tilghman.

When the camp commander's son, Lieutenant Justin E. Dimick, left Fort Warren for active duty in the field with the Second U.S.

The song was carried to the Army of the Potomac by the men of the "Webster Regiment" (12th Massachusetts Infantry), who had mustered in at Fort Warren.

[2] A plaque at the fort states that the southeast bastion was roofed over at this time to create a rare (possibly unique) casemated 15-inch Rodman gun battery.

[10] Different 10-inch M1888 guns, including two from Battery Reilly at Fort Adams in Rhode Island and two from storage, replaced these weapons in 1919.

[9] During World War II, the fort served as a control center for Boston Harbor's south mine field, a precaution taken in anticipation of potential attacks by Kriegsmarine U-boats.

[11] At that time, Fort Warren was garrisoned by the 241st Coast Artillery Regiment (Harbor Defense), a Massachusetts National Guard unit that was federalized in September, 1940.

The island offers a well-stocked snack bar, water fountains, and a large number of composting toilets.

There is also a museum located in the old mine storehouse (the red brick building opposite the ferry dock), a number of picnic tables, and a children's play structure.

The Commonwealth's only Confederate memorial, a headstone which commemorates 13 southern soldiers who died while imprisoned during the Civil War at the fort was housed on the island until 2017.