Saint John’s Seminary was founded by Archbishop John J. Williams in 1884, and chartered as a corporation doing business as a graduate school by an act of the Massachusetts legislature. The purpose of the seminary was to train priests for the Archdiocese of Boston and other dioceses of New England. Prior to this, Boston and the newly founded dioceses of Burlington, Portland, and Springfield sent their seminarians to study for priestly formation in Baltimore, Quebec City, and Europe.

In March of 1880, Archbishop Williams had acquired the 50 acre Stanwood Estate, near the present day Lake Street in Brighton. Williams, looking back on his own formation with fondness, invited the Sulpician Fathers to staff the seminary. Work began on what would be Saint John’s Hall in April of 1881, and continued for three years. Originally designed to hold 200 students, the plans were simplified, due to construction costs, but ample space was reserved for the future expansion of the seminary. Saint John’s Hall was ready for occupancy in May 1884, with room for 100 seminarians. The Sulpicians, who comprised the faculty and spiritual directors, came from Baltimore and from Paris. They brought with them a number of books and pieces of artwork; most notably they brought the statue of the Madonna and Child that is found in the courtyard, a replica of their cherished Madonna in the church of Saint Sulpice in Paris.

As the years passed, enrollment increased, and by 1895, the seminary was filled beyond capacity, with an enrollment 135 students. The Sulpicians continued to lead Saint John’s Seminary until 1911, when Archbishop William O’Connell replaced them with a faculty comprised of eleven priests of the archdiocese.

Saint John’s Chapel was not part of the original seminary construction. It was built in 1899, and constructed by the Boston firm of Maginnis and Walsh. The beautiful artwork which adorns the chapel was painted by Gonippo Raggi. The chapel, with its great beauty, remarkable pipe organ, and sonorous acoustics, has provided a fitting setting for the heart of the seminary.

Saint John’s Seminary went through another expansion and renovation in the 1920s. Saint John’s Hall was expanded, adding more rooms for students. The current refectory and kitchen, as well as new heating boilers and a convent for the sisters who served the seminary were also added at this time. A number of other buildings were constructed on the campus around the seminary during the first half of the Twentieth Century. This construction included facilities which housed several archdiocesan offices, including the chancery building, making the seminary and its grounds the heart of the Archdiocese of Boston for most of the 20th century.

For most of its existence, Saint John’s has enjoyed a healthy enrollment and a privileged role among the New England dioceses. Many of these dioceses have had an entire generation of their presbyterate formed at Saint John’s.

From 1970 until the turn of the 21st century, enrollment at Saint John’s, like all Roman Catholic seminaries, declined. By 1998 Saint John’s Hall was in need of modern systems and improved use of space. Under the direction of Cardinal Bernard Law, a major renovation of the hall was undertaken. Systems were replaced, modern bathroom facilities were installed and improvements were made to the common areas and classrooms.

In 2002, Saint John’s College Seminary closed its doors. In addition, in 2004 and again in 2007 Boston College purchased most of the real estate that was owned by the seminary. During this time, a renewed effort was made to build up the seminary program in the model articulated by Pope John Paul II. The Holy Father had called for excellence in Four Pillars of Formation: the Spiritual, Intellectual, Pastoral and Human aspects of priestly preparation. As a fruit of this effort, enrollment has increased dramatically, from a low of 42 in 2006 to over 100 at the start of the 2010 academic year. This increased enrollment includes resident seminarians from Boston and from other dioceses of New England, as well as international seminarians, and members of religious orders who attend classes at Saint John’s while residing with their respective houses of formation.