Milton was elected to become chancellor and chief executive officer of Reformed Theological Seminary on September 2, 2010, and officially assumed those duties on June 1, 2012, succeeding the Reverend Robert "Ric" Cannada, Jr. The investiture and inauguration service was held on September 14, 2012. Prior to becoming chancellor, Milton was President of RTS-Charlotte, elected in 2007, interim president of RTS Orlando, and the James M. Baird, Jr. Chair of Pastoral Theology since 2009. He retained the Chair of Pastoral Theology with his election as Chancellor. On March 13, 2013, it was announced that the Executive Committee of the Seminary granted a retirement from the position in order to seek recovery from a chronic illness (Dysautonomia) that had become increasingly debilitating. The move was described as compassionate in order for Milton to fully recover and be able to return to ministry. Milton wrote a theological reflection on the illness called, "Difficult but Necessary: Relinquishing Leadership in Winter to Renew Ministry in a New Season." Milton remained an adjunct member of the faculty. Milton is a faculty member and speaker with the Intercollegiate Studies Institute, and is a contributor to the Center for Vision and Values, a conservative think tank, at Grove City College. He is a contributing editor to and contributing writer for Preaching.com. He is, also, an adjunct faculty member of Belhaven University and holds the chair of missions and evangelism at Erskine Theological Seminary. In addition to devotional and Biblical themes, Milton has written commentaries on Christian faith in the public square. The Billy Graham Evangelistic Association invited Milton to write the theological affirmation for the Billy Graham final crusade, ""My Hope"". Milton was invited by President Ronald Reagan's son, Michael Reagan, to speak at the Reagan Center in Santa Barbara, California. He spoke on September 26, 2013, at the Reagan Center, before the guests of the Young America's Foundation, on the topic of "What the Legacy of Ronald Reagan Can Teach Us Today about Religious Liberty." Milton has presented and published peer-reviewed academic papers at American Society of Church History (ASCH), the Evangelical Theological Society. Milton's published "Curriculum Vitae" lists him as a member of the Society of Biblical Literature. John Donne Society, and the John Milton (American) Society. He was Senior Editor of the "U.S. Army Chaplain Corps Journal".