The St. Peter’s College Seminary was established primarily because of a felt need for priests in the Diocese of San Pablo. Until the late 1960’s, the province of Laguna was administered by the then Diocese of Lipa, now an Archdiocese. Most priests serving in Laguna came from other provinces since there were very few native-born priests of Laguna.

Following its canonical erection on November 28, 1966, the Diocese of San Pablo began its ecclesiastical functions and ministries under the leadership of its first Bishop Most Rev. Pedro Bantigue, J.C.D., D.D. In its early years of existence, the diocese established the San Pablo minor Seminary in response to the felt need for vocation to the priesthood. This site, with a total land area of 32,949 square meters, was donated by PAZ CORNISTA CATIPON to the ROMAN CATHOLIC APOSTOLIC DIOCESE OF SAN PABLO on June 05, 1967.

In 1981, a major seminary was established. Named ST. PETER’S COLLEGE SEMINARY, to emphasize the bond of faithful obedience rendered by the diocese to St. Peter the Apostle and his successors. It was inaugurated on July 06, 1981 under the administration of its first Rector, Most Rev. Msgr. Elias O. Poblete, J.C.D., M.Ed., Ph.D., with 29 seminarians. In the first three years, the major seminary was housed at the back of Liceo de San Pablo building. In the school year 1985-1986, after the minor seminary was phased out, the College Department and the Institute of Formation were transferred to their present site.

On February 22, 2011, the St. Peter's College Seminary celebrated its 30th year anniversary in the presence of the Most. Rev. Leo M. Drona, SDB,DD and the presence of the alumni.