When World War II began, Fechteler was operations officer for Destroyer Command. From 1941 to 1943, he served as assistant director of the navy's personnel bureau, and from 1943 to 1944 he commanded the battleship Indiana in the Pacific. In January 1944, Fechteler won promotion to rear admiral and took command of Amphibious Group 8 of the Seventh Fleet Amphibious Force. During the New Guinea Campaign, he directed amphibious operations in Biak (May 1944) and Sansapar (July 1944), and he directed the landings on Luzon and Palawan during the Philippines Campaign.
Promoted to vice admiral after the war, Fechteler served from 1946 to 1947 as commander of battleships and cruisers in the Atlantic Fleet. He then spent three years in Washington as deputy chief of naval operations for personnel. Appointed commander in chief of the Atlantic Fleet in 1950, the following year he unexpectedly became chief of naval operations (CNO) and a full admiral when the incumbent CNO, Admiral Forrest Sherman, suddenly suffered a fatal heart attack. From 1953 until he retired in July 1956, Fechteler was commander in chief of North Atlantic Treaty Organization (NATO) Forces Southern Europe. He died at Bethesda, Maryland, on 4 July 1967.
Barbey, Daniel E. MacArthur's Amphibious Navy: Seventh Amphibious Force Operations, 1943–45. Annapolis, MD: Naval Institute Press, 1969.; Hoyt, Edwin P. How They Won the War in the Pacific: Nimitz and His Admirals. New York: Weybright and Talley, 1970.; Kennedy, Gerald. "William Morrow Fechteler 16 August 1951–17 August 1953." In Robert William Love Jr., ed., The Chiefs of Naval Operations, 235–241. Annapolis, MD: Naval Institute Press, 1980.; Morison, Samuel Eliot. History of United States Naval Operations in World War II. Vol. 5, The Struggle for Guadalcanal, August 1942–February 1943. Boston: Little, Brown, 1949.; Morison, Samuel Eliot. History of United States Naval Operations in World War II. Vol. 13, The Liberation of the Philippines: Luzon, Minadanao, the Visayas, 1944–1945. Boston: Little, Brown, 1953.; Truscott, Lucian K., Jr. The Twilight of the U.S. Cavalry: Life in the Old Army, 1917–1942. Edited and with Preface by Lucian K. Truscott III and Foreword by Edward M. Coffman. Lawrence: University Press of Kansas, 1989.