After retiring from the NFL, McKee embarked on a career of college and high school coaching, teaching, and athletics administration. He started as an assistant coach at the University of Rochester, doing baseball, basketball, and football. He went on to coach high school football at Rome Free Academy, Vernon-Verona-Sherrill, and Rush-Henrietta, all in upstate New York. Between his years at V-V-S and R-H, he was an assistant football coach under John Yovicsin at Harvard (1960-1963). He started the R-H football program with an undefeated freshman team (1964) that continued undefeated the following season. From the fall when that team became seniors until McKee retired from coaching (1968-1972), the five full varsity teams he coached had a record of 37-3 and either won or tied for five conference championships.