The American Civil War broke out in April 1861, and Clitz served extensively in operations related to the Union blockade of the Confederate States of America. Promoted to commander on 16 July 1862, he was the commanding officer of the steam gunboat in the North Atlantic Blockading Squadron in 1863 and later that year of the steam sloop-of-war in the East Gulf Blockading Squadron. He commanded the new sidewheel gunboat in the North Atlantic Blockading Squadron from 1864 to 1865 and led her in both the First Battle of Fort Fisher in December 1864 and the Second Battle of Fort Fisher in January 1865, both of them attacks against Fort Fisher, one of the fortifications guarding Wilmington, North Carolina. In a dispatch of 28 January 1865, Rear Admiral David Dixon Porter commended him for his actions at Fort Fisher and recommended him for promotion.