In late 1941, Kinkaid was promoted to rear admiral and took command of Cruiser Division 6. In March 1942, he led his ships in raids on Rabaul and New Guinea, then participated in the May Battle of the Coral Sea and the June Battle of Midway. In August 1942, Kinkaid assumed command of Task Force 16, centered on the carrier Enterprise, and took part in the invasion of Guadalcanal and the Battles of the Eastern Solomons and the Santa Cruz Islands. In January 1943, Kinkaid took command of the North Pacific Force in Alaskan waters, his ships participating in the recapture from the Japanese of the Aleutian islands of Attu and Kiska.
Promoted to vice admiral, Kinkaid was put in charge of the Seventh Fleet, "MacArthur's Navy," in November 1943, with the mission of providing amphibious lift and protection to General Douglas MacArthur's Southwest Pacific Area forces on their approach to the Philippines. Seventh Fleet then participated in the defense of landings at Leyte by destroying attacking Japanese forces in Surigao Strait. In January 1945, Kinkaid led Seventh Fleet in the invasion of Luzon at Lingayen Gulf. Promoted to admiral in April, he took the surrender of Japanese forces in Korea in September.
Following World War II, Kinkaid briefly commanded the Eastern Sea Frontier and then the Sixteenth (Reserve) Fleet. He retired in May 1950 and died in Bethesda, Maryland, on 17 November 1972.
Belote, James H., and William M. Belote. Titans of the Seas: The Development and Operations of Japanese and American Carrier Task Forces during World War II. New York: Harper and Row, 1975.; Wheeler, Gerald. "Admiral Thomas C. Kinkaid." In Stephen Howarth, ed., Men of War: Great Naval Leaders of World War II, 331–348. New York: St. Martin's Press, 1992.; Wheeler, Gerald. Kinkaid of the Seventh Fleet: A Biography of Admiral Thomas C. Kinkaid, U.S. Navy. Washington, DC: Naval Historical Center, U.S. Navy, 1995.