He began his teaching career at Lees-McRae College in Banner Elk, North Carolina, from 1961 to 1964, where he met and married a colleague, Jane Ellen Baucom, in 1962. After returning to Chapel Hill to complete his doctoral studies, he joined department of sociology at the University of Kentucky in Lexington in the fall of 1966. Connecting with the emerging field of Appalachian studies, he co-edited Appalachia in the Sixties with sociology graduate studentDavid Walls. He served as dean of undergraduate studies from 1978 to 1981, as special assistant to the chancellor in 1983-84, and was the first director of the Appalachian Center, which he was instrumental in helping organize, from 1979 to 1984. During this time he became an incorporator and first chair of the Appalachian Studies Conference.
President of Berea College
In 1984 he was appointed the seventh president of Berea College in Berea, Kentucky, the first president of the liberal arts college to come from a public university. During his tenure as president, Berea College reemphasized its historic commitment to African American and Appalachian students. The college also took initiatives to support women, including Jane Stephenson's New Opportunity School for Women. Faculty and staff salaries were increased significantly. John Stephenson established ties with a diverse group of notable people whom he brought to speak at Berea College, from Roots author Alex Haley, and Archbishop Desmond Tutu of South Africa, to the Dalai Lama. Stephenson established the Tibetan scholarship program, which supports students at Berea College from the Tibetan exile community in India. He was also a successful fundraiser; during his tenure as president, the Berea College endowment increased from $120 to $360 million. Stephenson retired in July 1994, several years after he was diagnosed with leukemia. He died suddenly after a viral infection in December 1994. He was selected as an American Council on Education Fellow in 1973-74, and as a Fulbright Senior Research Scholar in 1981, which he used for research in Scotland which was presented in his book, Ford: A Village in the West Highlands of Scotland. He served on boards of the Kentucky Literacy Foundation, the national Elderhostel program, the Frontier Nursing Service, and the Appalachian Regional Hospitals.