Johnston was born in Macon, Georgia, and taught composition and theory at the University of Illinois at Urbana–Champaign from 1951 to 1986, before retiring to North Carolina. During his time teaching, he was in contact with avant-garde figures such as John Cage, La Monte Young, and Iannis Xenakis. Johnston's students have included Stuart Saunders Smith, Neely Bruce, Thomas Albert, Michael Pisaro, Manfred Stahnke, and Kyle Gann. He also considered his practice of just intonation to have influenced other composers, including James Tenney and Larry Polansky. In 1946 he married dance band singer Dorothy Haines, but they soon divorced; he married artist Betty Hall in 1950 (she died in 2007).