After graduating from Harold L. Richards High School in Oak Lawn, Johnston attended the University of Illinois at Urbana-Champaign. He planned to study journalism, but became intrigued by an introductory geology class, and changed his major. His first geologic project was a study of the Precambrian rock that forms Michigan's Upper Peninsula. There he investigated the remains of an ancient volcano: a suite of metamorphosed basalts, a gabbroic sill, and volcanic roots in the form of a dioritic and gabbroic intrusion. The experience planted the seed of Johnston's passion for volcanoes. After working hard to learn the subject, he graduated with "Highest Honors and Distinction" in 1971.