Confederate forces took control at the beginning of the Civil War but did not further construction. They instead established batteries in the town of Fernandina and on Amelia and Cumberland Islands. Advancing US forces caused General Robert E. Lee to authorize withdrawal in early 1862.
On March 3, 1862 US troops regained control of the fort and continued construction but were unable to finish.
Fort Clinch was never fired upon or ever fired is shot in anger and sustained no damage during the U.S. Civil War.
In 1935, the state of Florida purchased 256 acres which included the abandoned fort and developed one of Florida's first State Parks. The civilian Conservation Corps restored the fort in the 1930s. It was formally opened to the public in 1938.
Ten U.S. Civil War period guns are mounted on period carriages and emplaced along the parapets as they would have been in that period. Four major buildings have been restored and interpreted including a two story barracks, single story prison and guardhouse, and a two story warehouse. The entrance to the fort includes a visitor center/gift shop and a small museum. Must see fortification.