St. Joseph’s Seminary participates in the St. Charles Borromeo Inter-diocesan Partnership created by the three diocesan bishops of New York, Brooklyn and Rockville Centre. On November 10, 2011 Timothy Cardinal Dolan, Most Rev. Nicholas DiMarzio and Most Rev. William Murphy signed a Joint Operating Agreement that acknowledged their earlier decision to collaborate on a single college and pre-theology program at the Cathedral Seminary House of Formation in Douglaston NY, and to move toward a common graduate level program of priestly formation at Dunwoodie.

The Joint Operating Agreement was subsequently modified by a Memorandum of Understanding (March 15, 2012) to include the aggregation of all degree programs, faculty and students (lay and permanent deacon candidates) of the Seminary of the Immaculate Conception (SIC), Huntington NY to St. Joseph’s Seminary (SJS). By August 31, 2013, SJS became the sole degree-granting Catholic seminary for the downstate New York region, operating on a main campus (Yonkers) and two additional locations (Huntington and Douglaston). The Boards of Trustees of the Partnership schools have agreed that SJS will serve their constituencies by offering the following degrees:

• Master of Divinity Degree and the Degree of Bachelor of Sacred Theology (S.T.B.) from the University of St. Thomas Aquinas (Angelicum) in Rome to seminarians at the main campus
• Master of Arts in Theology to seminarians and non-seminarian students at the main campus
• Master of Arts in Catholic Philosophical Studies to pre-theologians at the Cathedral Seminary House of Formation, Douglaston, NY, who are preparing for graduate-level theology by taking courses in philosophy as a part of their formation for the priesthood