Later, Joseph Fry became the commander of the new blockade-runner Agnes E. Fry, named after his wife. He made three successful voyages through the blockade of Wilmington, North Carolina, and was then run ashore with complete loss of the ship. Fry, however, was not steering the ship at the time as it was the pilot. The wreck lies not far from the Virginius. Fry and the crew escaped.
Fry's next command was of the CSS Morgan in Mobile Bay where he was highly complimented by General Dabney H. Maury for conspicuous bravery.