His spouse is Kim Floyd Johnson. Their children are Emory Brennis Johnson, Elizabeth Marie Johnson, and John Dee Johnson, III. His civic interests include Huntsville Symphony Orchestra Board of Trustees, 2005-2015; Auburn University College of Science and Mathematics Advisory Board, 2005-Present; Leadership Huntsville/Madison Class 15; and Huntsville Committee of 100, 2004-2010. His professional associations include Huntsville Hospital Chairman of Surgery, 2012-2014; American Association of Neurological Surgeons, 1998-Present; Southern Neurosurgical Society; and Medical Association of the State of Alabama. His hobbies include travel and photography.