The son of John and Margaret Whalen, Msgr. Whalen was born July 6, 1958 and raised with his brothers in Blessed Sacrament Parish, Staten Island. From Blessed Sacrament School he went to Msgr. Farrell High School where he later taught and was principal. He graduated from Cathedral College of the Immaculate Conception, Douglaston, with a degree in history and was then sent to the North American College, Rome where he studied at the Pontifical Gregorian University, where he earned his STB in 1983. He was ordained a deacon in St. Peter’s Basilica, Rome in April, 1983. Monsignor Whalen served as a deacon in the Diocese of Kakamega, Kenya which helped him to understand the richness of our Catholic faith in its diverse expressions.
He was ordained a priest on 23rd June 1984 in St. Patrick’s Cathedral by then-Archbishop John O’Connor. His summer assignments were in Resurrection, Rye and St. Joseph’s, Bronxville. He then returned to Rome to complete the licentiate in moral theology at the Academia Alfonsiana of the Pontifical Lateran University in 1985. Upon returning to the United States, he served in Resurrection Parish, Rye under the guidance of Monsignor Donald Pryor, whom he first knew as a young priest in Blessed Sacrament.
In 1987, he returned to his alma mater, Msgr. Farrell High School to teach religion and be chair of the Religion Department. In 1990, he was appointed secretary to John Cardinal O’Connor. He then returned to Rome to complete the doctorate in moral theology at the Academia Alfonsiana in 1995. He then began what would be twelve years teaching moral theology at St. Joseph’s Seminary, Dunwoodie while also serving as Vice Rector (1997-1998) of Dunwoodie and then Rector of St. John Neumann Seminary Residence, Riverdale (1998-2001).
During these years, he was a weekend and summer assistant at St. Clare’s Parish, Morris Park, The Bronx, serving the Italian speaking community. In May, 2001 he became pastor of St. Benedict’s Parish, Throggs Neck, The Bronx where he continued to serve the Italian speaking community and began outreach to the Spanish speaking community. After six years, he was named pastor of St. Joseph-St. Thomas Parish, Staten Island in 2007, where he served until being named principal of Msgr. Farrell High School in 2010. While principal, he also taught religion and foreign language. During these years he served as a weekend assistant at St. Charles and St. Ann’s along with serving the Spanish speaking community at St. Roch’s, all on Staten Island.
In January, 2019 Cardinal Dolan named him Vicar for Clergy.