In 1988, he received a further order from Cardinal Ratzinger (soon to become Pope Benedict XVI, the first Pope to resign in a millennium) directing him to give up all ministry to Gay persons which he refused to do in conscience. As a result, he was expelled by the Vatican from the Society of Jesus (Jesuits) for challenging the teachings of the Roman Catholic Church on the issue of homosexuality, and for refusing to give up his ministry and psychotherapy practice to Gay men and Lesbians. McNeill had been a Jesuit for nearly 40 years.
After enlisting in the U.S. Army during World War II at the age of seventeen, McNeill served in combat in the Third Army under General Patton and was captured in Germany in 1944. McNeill spent six months as a POW (Prisoner of War) until he was liberated in May of 1945. John enrolled in Canisius College in Buffalo after his discharge from the army and, upon graduating, entered the Society of Jesus in 1948. He was ordained a Jesuit priest in 1959.
In 1964, McNeill earned a Doctorate in Philosophy, with highest honors (Plus Grande Distinction), at Louvain University in Belgium. His doctoral thesis on the philosophical and religious thought of Maurice Blondel was published in 1966 as the first volume of the series Studies in the History of Christian Thought edited by Heiko Oberman and published by Brill Press in Leyden, Holland.
During his professional career, McNeill taught philosophy at LeMoyne College in Syracuse, NY, and in the doctorate program at Fordham University in NYC. In 1972, he joined the combined Woodstock Jesuit Seminary and Union Theological Seminary faculty as professor of Christian Ethics, specializing in Sexual Ethics.
In 1974, McNeill was co-founder of the New York City chapter of Dignity, a group for Catholic Gays and Lesbians. For over twenty-five years, he has been active in a ministry to Gay Christians through retreats, workshops, lectures, publications, etc. For twenty years John was a leader of semiannual retreats at the Kirkridge Retreat Center in Pennsylvania.