In December 1864, he participated in the First Battle of Fort Fisher, North Carolina. While clearing naval mines (then known as "torpedoes") to make way for Union ironclads, Horgan was lightly wounded by flying shards of wood when a Confederate artillery shell struck nearby. The next month, at the Second Battle of Fort Fisher, he was among a party from the "Tacony" which joined the January 15 assault against the fort. Wounded twice during this action, Horgan spent the next eight months in a hospital.