Milliken served on board the U.S.S. New Ironsides during the action in several attacks on Fort Fisher, 24 and 25 December 1864; and 13, 14 and 15 January 1865. The ship steamed in and took the lead in the ironclad division close inshore and immediately opened its starboard battery in a barrage of well-directed fire to cause several fires and explosions and dismount several guns during the first two days of fighting. Taken under fire as she steamed into position on 13 January, the New Ironsides fought all day and took on ammunition at night despite severe weather conditions. When the enemy came out of his bombproofs to defend the fort against the storming party, the ship's battery disabled nearly every gun on the fort facing the shore before the cease-fire orders were given by the flagship.