In 1917, C. V. Whitney enlisted for pilot training in the US Army Signal Corps. He required his father's written permission since he was under eighteen years of age. He trained at Princeton University and then in Dallas and Ft. Worth, Texas. He was commissioned a second lieutenant and assigned to Carruthers+ Field, Texas, where he was the youngest flight instructor in World War I. He rose to first lieutenant and chief instructor in advanced fighter tactics.

When the war ended, Whitney enrolled at Yale University and was a classmate of Juan Trippe. In June 1927 he joined a coalition of backers to finance Juan Trippe in forming Aviation Corporation of America to offer Caribbean air service from Florida. His stake was reportedly $3,150, and he became president of the corporation. Aviation Corporation of American merged with Pan American Airways and from 1931 until 1941 Whitney served as chairman of the board of the successor company, Pan Am. As chairman, Whitney oversaw Pan American Airway's expansion in the Pacific and participated in several historic flights across the Pacific and on to China.

When America entered World War II, C.V. Whitney reentered active duty in the Army Air Corps as a second lieutenant. He served as a staff intelligence officer in the Pacific, Indian and Middle Eastern theaters, rising to the rank of Colonel. The National Security Act of 1947 established the position of Assistant Secretary (Civil and Military-Diplomatic) of the Air Force, and Cornelius V. Whitney was appointed. He held the post until 1949 and was responsible for functions relating to civil and militarydiplomatic affairs, including policies affecting the Air Reserve and Air National Guard. His tenure as Assistant Secretary of the Air Force coincided with the Berlin Airlift. He then served as Undersecretary of Commerce from 1949-50.

In the 1930s, Whitney purchased Maple Hill, his father's horse farm outside Lexington and began a lifelong involvement with horse racing. Over the years, 450 stakes winners were bred or raised on the 1,000 acres of the Whitney Kentucky farm. In 1985 he received the Eclipse Award for lifetime achievements in thoroughbred horse racing.