During the Battle of Hampton Roads on 8 March 1862 in which CSS Virginia destroyed the Federal warships USS Cumberland and USS Congress, Patrick Henry attempted to take the latter’s surrender but was fired upon by shore batteries, and took a shell in her steam chest that killed four men. Towed out of action long enough to make repairs, she soon resumed her former position.
Patrick Henry was designated an academy ship in May 1862 and underwent appropriate alterations. In October 1863, Patrick Henry housed the floating Confederate States Naval Academy at Drewry’s Bluff, where instruction for 52 midshipmen began under the superintendency of LieutenantWilliam Harwar Parker. Numbers later increased to sixty, with thirteen teachers in attendance. Sometimes she took part in action with the midshipmen on board.
When Richmond was evacuated on 3 April 1865, Patrick Henry was burned to prevent capture. Her midshipmen were charged with the delivery of a treasury of some CS$500,000 to the new government seat of Danville, Virginia. When they were disbanded each were given $40 in gold to help them reach their homes.