He began his studies for the priesthood at Saint Joseph"s Seminary in Yonkers, and also studied at Saint Louis University in Saint Louis, Missouri, and at the University of Notre Dame in South Bend, Indiana.
He served as an auxiliary bishop of the Archdiocese of New York from 1970 to 1994. Ahern was ordained a priest of the Archdiocese of New York on January 27, 1945. His first assignment was as a curate at Saint Helena"s Church in The Bronx.
He then worked with the Archdiocesan Mission Band until 1955, when he became a curate at Saint Patrick"s Cathedral.
He taught at Saint Joseph"s Seminary before serving as secretary to Cardinal Francis Spellman from 1958 to 1967. He afterwards became pastor of Our Lady of Angels Church in the Bronx.
On February 3, 1970, Ahern was appointed Auxiliary Bishop of New York and Titular Bishop of Naiera by Pope Paul VI. He received his episcopal consecration on the following March 19 from Cardinal Terence Cooke, with Archbishop John Joseph Maguire and Bishop Edwin Broderick serving as co-consecrators, at Saint Patrick"s Cathedral. As an auxiliary bishop, he continued to serve at Our Lady of Angels Church and was also episcopal vicar for the Bronx.
He served as episcopal vicar for Staten Island and pastor of Blessed Sacrament Church from 1980 to 1990.
He then became archdiocesan vicar for development. After reaching the mandatory retirement age of 75, Ahern resigned as an auxiliary bishop on April 26, 1994. He was widely regarded as one of the foremost experts on the spirituality of Saint Thérèse de Lisieux.