Johnston was educated in reserve schools in Cape Croker and later sent, along with his sister Marilyn, to residential school in Spanish, Ontario. He wrote about his experience as a student at St. Peter Claver School for Boys in his 1988 book Indian School Days. After graduating high school as class valedictorian, he earned his B.A. with Honours from Loyola College (1954) and a high school teaching certificate from the Ontario College of Education (1962). In 1959, Johnston married Lucie Desroches, with whom he had three children – Miriam, Tibby and Geoffery.
