The Santee was refitted at the Boston Navy yard and recommissioned. It was then sent to Newport, Rhode island, to serve as a school ship for the midshipmen at the United States Naval Academy (USNA). The USNA had moved there from Annapolis, Maryland for safety during the war.
Midshipmen lived, studied and attended classes on the Santee and USS Constitution.
After the war, the USNA returned to Annapolis and the Santee with its midshipmen anchored near Fort Severn on 2 August 1865.
It continued use as a school ship. In 1866, it became a gunnery ship for mastering of naval armaments. After that, it also became a barracks ship for punishment and barracks for incoming fourth classmen.
Before dawn 2 April 1912, the Santee sank at its moorings in Annapolis. Efforts to refloat it were unsuccessful.
It was sold to Joseph G. Hitner of Philadelphia on 2 August 1912. It took six months to raise the Santee and 8 May 1913, it departed the Severn River under tow for Boston, Massachusetts where it was burned for the copper and brass in its hull.