Stirling served for the rest of the war in the North Atlantic Blockading Squadron as part of the Union Blockade of the Confederate States of America. His first duty was aboard the screw sloop-of-war until 13 April 1864, when "Shenandoah" began a period under repair in Philadelphia, Pennsylvania. He then served aboard the flagship of the North Atlantic Blockading Squadron, the monitor , on the James River in Virginia until reporting back aboard "Shenandoah" for duty when she returned to service in June 1864. Aboard "Shenandoah" he saw combat at Fort Fisher in North Carolina in both the First Battle of Fort Fisher in December 1864 and the Second Battle of Fort Fisher in January 1865 and remained on blockade duty through the end of the war in April 1865.