Born in Florence, Alabama, Shannon Johnston attended local public schools and then the University of the South in Sewanee, Tennessee, from which he graduated in 1981 with a bachelor's degree in philosophy and music.

He then led programs for young people at the University of North Alabama and with the Boys' Club of Brunswick, Georgia.

In 1990, he accepted a call as rector of Church of the Advent in Sumner, Mississippi, where he also began a prison ministry with the nearby Parchman State Penitentiary.

His outreach work received national recognition, and he also held various leadership posts in the Episcopal Diocese of Mississippi, including nine years as dean and two terms as president of the Standing Committee.

After judicial resolution of the long litigation concerning the attempts of certain conservative churches in Virginia to withdraw from the Diocese and associate with an African diocese with similar opposition to same-sex marriages, Bishop Johnston drew nationwide attention for his peacemaking with the pastor of one of the dissident congregations.