He enlisted in the United States Army Air Corps in 1940 and was deployed to the Pacific Theater. He was commissioned as a Second Lieutenant in 1941 and made an aerial navigator. He served two tours of duty in the Philippines and was promoted to First Lieutenant. During the Philippines Campaign, Whitcomb's base was overrun; he was captured by the Japanese and was beaten and tortured by his captors, but was able to escape. Recaptured a few days later, he escaped a second time and was hunted for several more days but was able to evade his pursuers. He escaped by swimming all night through shark-infested waters to an island unoccupied by the Japanese army. He was eventually able to secure passage to China under an assumed name where he made contact with the United States Army and was repatriated in December 1943. He wrote a book about his experience entitled "Escape from Corregidor", published in 1958. He was discharged from active duty in 1946, but he remained in the reserve military forces until 1977 holding the rank of colonel.