Father Holmes has been a professor of moral and sacramental theology since 1988. After ten years on the President's Executive Cabinet, he was the University's first vice president for Mission, interim dean of the Whitehead School of Diplomacy and International Relations, and executive vice president. He was also associate vice president for Academic Administration, chair of the Department of Religious Studies and vice chair of the Faculty Senate.
Having helped inaugurate an interdisciplinary therapeutic outpatient program for priests in 1992, he has recently returned to St. Vincent's Hospital in Westchester as the program's spiritual director.
For the last several years, Father Holmes' interests include homiletics (the teaching of liturgical preaching) as well as preparing priests for their role as pastor and, after receiving a generous grant from the Lilly Endowment, he coordinates an annual conference for new pastors where he teaches a "theology of management" and introduces 14 presentations on all facets of parish management.
Teaching courses in moral theology (Contemporary Moral Issues and Theology of Sexuality), Father Holmes teaches courses in sacramental and spiritual theology, as well (Theology of Marriage which has been accepted as a Signature III course in the Core Curriculum; Sign, Symbol and Sacrament; and Mind and Spirit). The most important measure of his teaching and learning philosophy is his desire to create a "learning community" in every classroom where both professor and students feel a genuine responsibility to each other.
- STD, Pontifical University of St. Thomas Aquinas (Rome, Italy)
- STL, Pontifical Lateran University (Rome, Italy)
- STM, Yale University
In November 2010 and in response to a proposal submitted by Father Holmes, Lilly Endowment awarded Seton Hall University $722,000 to fund the Toolbox for Pastoral Management and the creation of a Web-based "virtual community of practice" to assist American priests in their parish management responsibilities.
In June 2010, a resolution of the University's Board of Regents named Father Holmes "Distinguished University Professor of Servant Leadership."
In 1999-2000, Father Holmes was the first to hold the Carl J. Peter Chair of Preaching at the North American College in Rome.