The area of NSB Kings Bay began as plantation land, and later a minor fortified position for American forces fighting the British in the War of 1812. The area had no real involvement in the Civil War.

In 1954 Kings Bay was developed as a US Army ocean terminal for ammunition shipments in the event of a national emergency. It was used for Army unit prepositioning in the event of war during the Cuban Missile Crisis of 1962, and disaster relief after Hurricane Dora. The emergency it was built for never came, and the US Navy acquired the land in the 1970s, to replace a US sub base in Spain.

The story of the Navy's efforts to select the best sub base site on the East Coast is long, complex, and not very interesting. The site was rebuilt in the late 1970s, and the first submarine ported, the USS James Monroe at NSB Kings Bay in July 1979. This was the largest peacetime construction project the US Navy has ever undertaken. In the mid-1980s the decision was made to use Kings Bay as a Trident base, homeporting Ohio-class submarines.

In 1989 NSB Kings Bay finished converting to a Trident base, and since then has been the primary Trident sub base on the US East Coast, homeporting ballistic missile and guided missile nuclear submarines. The conversion to a Trident base also brought an expansion of the base's facilities, adding the Trident Training Facility, Trident Refit Facility, and the Strategic Weapons Facility Atlantic, and additional housing, and a new training pool.

The drawdown after the end of the Cold War led to some force shifting and reduction, and the relocating of subs to the West Coast. In the early 2000s the four oldest Ohio-class subs were converted into guided missile subs with berthing for troops. NSB Kings Bay remains one of the keystones of the submarine fleet.