The Civil War brought him back into the service and he soon distinguished himself as an officer of extraordinary initiative and courage. Promoted lieutenant in mid-1862, Cushing served as executive officer of gunboat Commodore Perry, then commanded tug Ellis and gunboats Commodore Barney, Shokokon and Monticello. During this time, he led several daring reconnaissance and raiding excursions into Confederate territories.
On the night of 27–28 October 1864, Cushing commanded a steam launch in attacking and sinking Confederate ironclad ram Albemarle at Plymouth, North Carolina—an action that made him a national celebrity. Promoted lieutenant commander, in January 1865, he helped lead the Navy landing force in the conquest of Fort Fisher, NC, again distinguishing himself.
After the war, Cushing held numerous other posts until his always-delicate health gave way. He died on 17 December 1874.