Whitehorn was born in a sod house in Spencer, Nebraska, on the prairie, the son of a farmer and part-time school teacher.
He graduated from Doane College in Crete, Nebraska, and won a scholarship to attend Harvard University Medical School.
In 1938, Whitehorn was hired to lead the Department of Psychiatry at Washington University School of Medicine in St. Louis, Missouri where he remained for three years.
He moved to the Johns Hopkins School of Medicine in Baltimore, Maryland as the Henry Phipps Professor of Psychiatry, succeeding Adolf Meyer.
In 1955, Whitehorn described his philosophy and methods of psychiatry in his Salmon lectureship of the New York Academy of Medicine, later published under the title Psychiatric Education and Progress.
Among his private papers stored at the American Psychiatric Association (APA) was a note describing how he was collected blood from patients for a study on humoral changes and emotion.
Whitehorn, John C. "Guide to Interviewing and Clinical Personality Study," Archives of Neurology and Psychiatry, 52: September 3, 1944, p. 197–216.