The island was declared a United States military reservation in 1847, and nine years later Congress authorized construction of a fort.

A site on the north shore, approximately 500 feet (152 m) from the western tip of the island, was eventually selected as the location for the fort.

The militia soon abandoned the island; and it remained deserted until early June 1861, when Confederate troops returned and mounted several cannons.

During the remainder of the summer of 1861, the Confederate contingent on the island worked with sandbags and timber to strengthen the walls of the unfinished fort.

After U.S. authorities regained control of the island (1861–62), bricks were shipped from New England, down the East Coast and around the Florida peninsula.

Fort Massachusetts had lain at the water's edge; and wave action, not to mention the salt air, had seriously eroded the historic mortar, especially around the northeast bastion.

A "Save the Fort" movement started by Mississippians in the 1960s led to the establishment of Gulf Islands National Seashore.

But, unlike the Cape Hatteras Light, Fort Massachusetts is made of tons of brick and concrete, and it could not be relocated.

To save tax dollars, the National Park Service piggy-backs on dredge projects of the U.S. Army Corps of Engineers.

In addition, employees from the Historic Preservation Training Center stepped ashore in December 2001 to re-point, replace, and reset, as needed, the brick walls of the fort—which hadn't been maintained since 1866.