Father McAfee was born December 13, 1943, in Detroit, Michigan. He attended St. David Elementary School and Sacred Heart High School, both in Detroit. He graduated from Catholic University in Washington in 1966. He attended the Gregorian Institute of America in the summer of 1962 and Catholic University's graduate school from 1966-67. He earned a master's degree in Religious Studies from St. Thomas Aquinas University in Rome. He went on to attend the Theological College at Catholic University for graduate studies in Philosophy and Theology from 1967-71.