Applewhite attended Corpus Christi High School and Austin College; at the latter school, he was active in several student organizations and was moderately religious. He earned a bachelor's degree in philosophy in 1952 and subsequently enrolled at Union Presbyterian Seminary to study theology, hoping to become a minister. He married Anne Pearce around that time, and they later had two children, Mark and Lane. Early in his seminary studies, Applewhite decided to leave the school to pursue a career in music, becoming the music director of a Presbyterian church in North Carolina. He was a baritone singer and enjoyed spirituals and the music of Handel.