Saint John’s Seminary is sponsored by the Archdiocese of Boston. It observes the applicable norms of the Holy See and the United States Conference of Catholic Bishops in defining and realizing its mission.

The primary mission of Saint John's Seminary is to prepare candidates for ordination as diocesan priests in the Roman Catholic Church and to recommend them to sending bishops. The Seminary enrolls candidates for the priesthood from Institutes of Consecrated Life and Societies of Apostolic Life in its several degree programs of priestly formation.