After graduation, McKee coached at North Carolina A&M from 1899 to 1900 to a record 1–7–2. In 1901, he coached at Georgia Tech and did much better, finishing with a record of 4–0–1. After Georgia Tech's season ended, McKee joined the Georgia football staff in their preparation against Auburn. Incidentally, McKee sued the Georgia Institute of Technology in June 1902 for breach of contract for the amount of $500.
Following his football coaching career, he received a medical degree from the University of Maryland in 1907, and entered into medical practice in his hometown of Raleigh. During World War I, McKee achieved the rank of major in the American Expeditionary Forces as a field surgeon with the 1st Gas Regiment. McKee returned to Raleigh after the war where he was the city physician until 1948. “Dr. John” was very well known throughout the state of North Carolina for his gruff but compassionate sense of humor and his propensity to curse. He loved to drive a T-Model Ford automobile. When Ford discontinued the car, McKee refused to drive any longer despite the fact he was issued a new Buick every year by the Raleigh city fathers, and police officers and firemen took him on his rounds every morning. McKee died in Morganton, North Carolina on April 22, 1950, at the home of his son, Dr. John S. McKee III, superintendent of the Broughton State Mental Hospital.