The Confederate battery again abandoned the island in mid-September. The Union occupied the island and used it as a staging area for the campaign against New Orleans in the spring of 1862. During the campaign, as many as 18,000 U.S. troops were stationed on the island. Through the remainder of the war Union ships stopped at the island for repairs and to pick up supplies. The 1st Louisiana Native Guard, one of the first black regiments in the United States Army, were recruited in Louisiana and stationed there for almost three years. The island's harsh environment took its toll on many of the men. More than 230 Union soldiers eventually died and were buried on Ship Island during the Civil War. The remains of many of the casualties were later reburied at Chalmette National Cemetery, near New Orleans.
The Corps of Engineers finished the fort shortly after the war. The fort was a lonely outpost, manned by a an ordnance-sergeant until 1903. After 1903, the lighthouse keeper was responsible for maintaining the fort in a state of readiness should it ever be needed for coastal defense.