A battleship captain for most of 1941,Wilkinson became director of Naval Intelligence in October of that year. He escaped blame for Pearl Harbor because the evaluation and dissemination of intelligence was another bureau's responsibility, even though his office gathered intelligence information. Promoted to rear admiral in April 1942, Wilkinson took command of Battleship Division 2 that August, and in January 1943, he became deputy commander of the South Pacific Force, under Admiral William F. Halsey. During the Solomon Islands Campaign, he not only solved numerous operational problems but also exercised his considerable diplomatic skills on often contentious Allied colleagues.
From July 1943 to late 1945, Wilkinson commanded the 3rd Amphibious Force, with headquarters at Guadalcanal. He firmly advocated a "leapfrogging" strategy of avoiding heavily fortified Japanese-held islands and concentrating on easier targets. Wilkinson successfully organized landings on Cape Torokina, Green Islands, New Georgia, Vella Lavella, Treasury Island, Bougainville, Palau Island, Leyte, and Lingayen Gulf on Luzon, winning promotion to vice admiral in September 1944. His final wartime assignment was to airlift General Robert Eichelberger's Eighth Army to Tokyo Bay on the day of the Japanese surrender in September 1945.
Returning to Washington, Wilkinson became a member of the Joint Chiefs of Staff joint strategic survey committee. He drowned accidentally when his automobile plunged off the car ferry at Norfolk, Virginia, on 21 February 1946.
Dorwart, Jeffery. Conflict of Duty: The U.S. Navy's Intelligence Dilemma, 1919–1945. Annapolis, MD: Naval Institute Press, 1983.; Hoyt, Edwin P. How They Won the War in the Pacific: Nimitz and His Admirals. New York: Weybright and Talley, 1970.; 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.