After the war, Johnston studied for two years at a private academy in Prairie Home, Missouri before entering the Kemper Family School in fall 1867.
He studied under Professor Frederick T. Kemper until 1871, then was admitted to the senior class of the University of Missouri.
Johnston was named Kemper president and placed in control of the school.
He also made the seminal decision to convert Kemper to a military school.
Johnston introduced the Standard of Honor in 1915, began a formal ROTC program in 1916, and added a junior college in 1923.