[1] He was the son of a local attorney and cotton planter James Steptoe Johnston and his wife Louisa Clarissa Bridges Newman.

He saw action at the Second Battle of Bull Run and at Antietam before being captured by Union forces and spending one year as a prisoner of war.

In 1887, he was elected as the second bishop of the missionary district of west Texas and was awarded a Doctorate of Divinity from the University of the South in the same year.

Johnston was also responsible for the integration of the district, and admitted a congregation of African-Americans who had previously been affiliated with the Methodist Church.

A liberal with moderate Tractarian influences, Johnston was committed to dialogue with the Roman Catholic Church (by far the largest religious group in Southern and Western Texas) and wrote on several occasions to Vatican expressing his desire for Christian unity.