Construction of coastal batteries was authorized by Congress under the $50 million Harbor Fortification Defense Act of 1898. Fort Fremont was built by the Corps of Engineers on condemned private property with construction starting in 1899. Former owners of portions of the condemned land were Ellen A. Crofut, F.A. Dran, Jacob Meyers, Jack Freeman, July Fripp, Andrew Jenkins and Ellen Williams. The Corps of Engineers hired labor from the Beaufort area to build the military complex. In 1900, Fort Fremont was turned over to the Coast Artillery. The National Register of Historic Places documentation states that "Fort Fremont is one of only two extant Spanish–American War fortifications which retain their character from that period."
The complex at Fort Fremont consisted of almost 170 acres of land with numerous outbuildings, including an Administration building, guard house, barracks, hospital, stable, mess hall, bakery, commissary, post exchange, lavatory, and water tower. Of these, only the 10 inch battery, the rapid-fire battery and the brick hospital built in 1906 survive. All the other structures were made of wood and were demolished at various points before 1989 when documentation was submitted to the National Register of Historic Places.
The garrison's single artillery company manned three 10-inch disappearing guns and two 4.7-inch rapid fire guns. Much of the bastions and the concrete emplacements for the guns remain today. (The March 2, 1899 issue of The Palmetto Post told that "a large force of laborers" was at work on the fortifications, that the 4.7-inch guns had already been mounted, and the emplacements had been completed for the larger weapons).
As early as 1906, however, the War Department gave serious consideration to the closing of Fort Fremont, due to budgetary constraints.
Regarding reports that Fort Fremont would be sold or abandoned, the April 16, 1912 issue of the Beaufort Gazette quoted the Assistant Secretary of War: "... I have the honor to inform you that no such action is contemplated at present. A small detachment of soldiers had been serving as caretakers at the fort after troops stationed there had been reassigned to Galveston the previous year.
A December 7, 1921 Charleston News and Courier article reported that the U.S. Treasury Department requested Fort Fremont from the U.S. War Department for use as a quarantine station. The property had by then been placed on the Secretary of War's list of properties no longer needed for military purposes and available for sale. Fort Fremont was subsequently deactivated as a military installation in 1921.
- "About Fort Fremont". Beaufort County Library. Retrieved 26 October 2009.