[2][3] Managed by the United States Department of Veterans Affairs, it encompasses 44.1 acres (17.8 ha), and as of 2024, had over 28,725 interments.

The original interments in the cemetery were men who died in nearby Union hospitals during the occupation of the area early in the Civil War, mainly in 1861, following the Battle of Port Royal.

[5] In 1987, the remains of nineteen Union soldiers of the all black Massachusetts 55th Volunteer Infantry were discovered on Folly Island, South Carolina.

The Items discovered included leather shoes, rubberized canvas, wood staves and animal bone.

On May 29, 1989, the 54th soldiers were reinterred in the Beaufort National Cemetery with full military honors.