Early centuries in Manila

In 1592, the King enjoined that the pertinent decree of Trent be implemented in the Indies. He ordered all archbishops and bishops of the Indies to found and support seminaries decreed by the Council of Trent for the formation of a local (native) clergy.

Since the Philippines was then under the "Patronato Real" system, on April 28, 1702, King ordered the establishment of a seminary in Manila for eight seminarians. However, this plan was modified by Giovanni Battista Sidoti, an Italian priest accompanying Archbishop Charles Thomas Maillard de Tournon, papal legate to Peking, on the way to China. He worked for the erection in Manila of an Asian regional seminary for seventy-two seminarians of the Far East, with the approval of Archbishop Diego Camacho y Ávila. The seminary was named Real Colegio Seminario de San Clemente in honor of Pope Clement XI. Having learned of the development, the King ordered the closure and demolition of the seminary building, the execution of his original plan, and the transfer of Archbishop Camacho to Mexico.

From 1702 to 1730, seminarians took their courses of philosophy and theology at the Colegio de San Jose and Colegio de Santo Tomas. The number of seminarians increased several times.

On December 8, 1707, Archbishop Francisco de la Cuesta, Camacho's successor, opened the seminary. In 1715, he renamed the seminary to Real Seminario de San Felipe in honor of the King's patron saint. It was located in front of the Archbishop's Palace in Intramuros.

In 1728, Archbishop Carlos Bermúdez de Castro had a dispute with the governor-general over his right to nominate professors in San Felipe. He argued that the seminary was an ecclesiastical institution to be administered by the archbishop in conformity with the decrees of the Council of Trent and the laws of the Indies. His successor, Archbishop Juan Angel Rodríguez, continued de Castro's fight over the archbishop's right to guide the seminary. However, the civil authorities, under the pretext of Patronato Real, rebuffed them.

The impetus for a review of how the Patronato Real administered the seminary came when Bishop Miguel Lino de Espeleta of Cebu became acting governor-general of the Philippines from 1759 to 1761. He insisted that the royal treasury pay its obligations to the seminary which amounted to 54,000 pesos from 1705 to 1759. The royal treasury had committed 1,200 pesos for the yearly maintenance of the seminary. Hence, during the fifty-four years of the seminary, the royal contribution to the seminary averaged only 200 pesos a year.

The British invasion in 1762 dispersed the seminarians. It was only on January 25, 1768, that the seminary was re-opened by Archbishop Basílio Sancho de Santa Justa y Rufina, naming it Colegio Seminario Ecclesiástico de Manila. It was placed under the royal patronage of King Charles II. On November 16, 1778, the King ordered a visitation of the seminary. As a result, reforms were instituted, and the magnificent buildings of the expelled Jesuits, the Church and Colegio de San Ignacio were assigned to the diocesan seminary. For some thirty years (1784–1817), the Colegio de San José and the diocesan seminary, which began to be called in 1786 as Real Seminario Conciliar de San Carlos in honor of the King, existed side by side. San Carlos was located from 1784 to 1880 on Calle Real de Palacio (now General Luna Street) and Calle Escuela (now Victoria Street).

The Congregation of the Mission (CM), familiarly known as Vincentian Fathers, took charge over the seminary on August 2, 1862, under the patronage of Queen Isabella II and with the support of Archbishop Gregorio Melitón Martínez de Santa Cruz. Gregorio Velasco became the first Vincentian Rector of the conciliar seminary.

Earthquakes in 1852, 1863, 1880, and 2013 damaged the Church of San Ignacio and the seminary building itself. Following the last earthquake, the Vincentians temporarily moved their charges to their Casa del Ocampo at 959 Calle San Marcelino (1880–1883).

In 1883, Archbishop Pedro Payo, O.P constructed a new seminary building between the new Jesuit church of San Ignacio and the Archbishop's property on Calle Arzobispo. The building was rented in 1925 by Ateneo de Manila and was called Patio de San Javier. At present, it is the quarters for the employees of the Intramuros guest house of the archdiocese.

In 1897, the seminary moved to a new building built under the direction of Archbishop Bernardino Nozaleda. It occupied a whole block bordered by Beaterio, Anda, and Real de Palacio (Gen. Luna) Streets. The seminary stayed in this building for only a year (1897–1898). With the outbreak of the Philippine Revolution, the archbishop ordered its closure. The building, for a while leased by the Americans, became known as Saint Paul's Hospital, under the charge of Saint Paul de Chartres Sisters and later the Maryknoll Sisters.

Between the years 1900–1911, the seminary existed in an old building along Calle Arzobispo beside the new San Ignacio Church. On May 20, 1905, the administration of the seminary was turned over by the American Archbishop Jeremiah Harty to the Jesuits. This arrangement under the Jesuits lasted for only six years until August 17, 1911. In the next two years, San Carlos was fused with Seminario de San Javier (the name given by the Jesuits, upon their return to the Philippines, to Colegio de San José) on Padre Faura Street in Ermita. The few seminarians then went to San Javier for their studies until 1913, when San Javier was closed.

Years in Mandaluyong

For economic reasons, on May 19, 1913, Harty decided to transfer seminarians to a renovated building in the then town of Mandaluyong, which was constructed by the Augustinians in 1716 and had been abandoned since around 1900. In June 1913, the Vincentians were again put in charge of the seminary. The seminary's name in honor of San Carlos Borromeo was by then definite.

In 1927, to separate the major seminarians from the minor seminarians, San Carlos was again housed at Casa de Ocampo along San Marcelino (in the campus of Adamson University). In 1936, due to the construction of a new building in San Marcelino, the major seminarians joined the minor seminarians in Mandaluyong. The following years, San Carlos Seminary returned to San Marcelino in the newly constructed Central House of the Vincentian Fathers. In 1941, the major and minor seminarians were reunited under one campus in Mandaluyong. In December, the Second World War caused the closure of the campus, only to be reopened in 1946. But there were a huge number of enrollees that steps were taken in the postwar years.

Move to Makati

In 1916, Harty was succeeded by Archbishop Michael O'Doherty, who reigned until 1949. Cebu Archbishop Gabriel M. Reyes, who became the first Filipino Archbishop of Manila in 1949, planned and ordered the construction of the new San Carlos Seminary at Makati to accommodate the huge number of seminary students. In 1951, he blessed the cornerstone for the new building of San Carlos Seminary in Guadalupe Viejo village along Highway 54 (now Epifanio de los Santos Avenue or EDSA). On January 24, 1953, Cardinal Norman Thomas Gilroy, Archbishop of Sydney and papal legate to the First Plenary Council of the Philippines, blessed the new building. The Manila seminarians and professors transferred from Mandaluyong to the new San Carlos Seminary to begin the school year 1953–1954. The new seminary building was constructed to house the major and minor seminarians of the Archdiocese of Manila (Rizal, Cavite and Bulacan and Laguna were still included). The right wing would be occupied by the minor seminarians and the left wing by the major seminarians. In the middle of the building is the common chapel and in the basement, the refectory.

In 1951, the Congregation of the Immaculate Heart of Mary (CICM, known as the Belgian or Scheut Fathers) had been asked by Rome to take up the formation of the seminarians in Lipa, where Bishop Rufino J. Santos (later Archbishop of Manila in 1953 and the first Filipino cardinal in 1960) was then the administrator of the diocese. On June 10, 1953, it was announced that the CICM Fathers would take over San Carlos Seminary from the Vincentians, and with that San Carlos student body included the major seminarians (theology and philosophy) of Lipa, which were transferred to Makati. The transfer took place on the June 15 and 16 and on June 25, the new school year began with the Mass of the Holy Spirit.

In 1955, the minor seminarians were then separated from the philosophy and theology seminarians of San Carlos Seminary. They transferred to the newly erected minor seminary under the name of Our Lady of Guadalupe Minor Seminary, which was blessed on August 22, 1955. It was located a block away from San Carlos Seminary in the direction of the Pasig River, near the present day Guadalupe MRT station. In 1973, Cardinal Santos turned over the seminary administration from the CICM Fathers to the diocesan priests led by Oscar V. Cruz, who later became Auxiliary Bishop of Manila in 1976.

The construction of the new building of the San Carlos Graduate School of Theology and the Archbishop Gabriel M. Reyes Memorial Library began in 1985, and they were completed and blessed by Cardinal Sin and Cardinal Ricardo Vidal, Archbishop of Cebu, on June 29, 1987. In that same year, the two-winged edifice for the Holy Apostles Senior Seminary (HASS) and the San Lorenzo Ruiz Lay Formation Center (or LayForce) was constructed. The Lorenzo Mission Institute (LMI), aimed at forming priestly candidates for the missions to the Chinese communities was built in 1989. In 1990, Bahay-Pari, a house for priests, was put up for the ongoing formation, physical rest and spiritual rejuvenation for the Manila clergy. On March 13, 1995, the cornerstone of Holy Apostles Senior Seminary was laid to give way to the full-swing formation of the laity at the Layforce Building.

When Bishop Luis Antonio G. Tagle became Archbishop of Manila in 2011, he continued the vision of his predecessor Cardinal Rosales, to uplift and deepen the formation program of the seminarians through regular pastoral and theological updating and strengthening the seminary's thrust in human formation of the seminarians.

Some of the historic events that took place in San Carlos Seminary were the following: the Second Plenary Council of the Philippines (January 20 to February 17, 1991); the Sixth Plenary Assembly of the Federation of Asian Bishops' Conferences (January 10–19, 1995); the visit of Pope John Paul II (January 15, 1995); the National Pastoral Consultation on Church Renewal (January 20–27, 2001); and the Second National Rural Congress (July 7–8, 2008).

Through the years, the seminary has produced many dedicated and zealous men who have served for the mission of the church. Some of San Carlos Seminary's distinguished alumni are Gomburza priests Mariano Gómez and Jacinto Zamora, priest-martyrs executed by the Spanish government for supposed involvement in the 1872 Cavite Mutiny and thus inspired the Revolution; Cardinal Rufino Santos; and Ricardo Vidal, Cardinal Archbishop of Cebu.

The seminary is considered a national architectural heritage, since its architect during the building construction of 1951 to 1952 is Juan Nakpil, National Artist for Architecture.^[1]

A statue of the Ascension of Our Lord on the seminary grounds.

Propaedeutic Stage (Pre-College Department)

• Fresh high school graduates, college undergraduates and graduates, who are no more than 22 years of age, undergo this one-year period of rigid seminary orientation. They learn the rubrics of prayer life, community living, study habits, and personal growth. This stage was used to be called the Juniorate Department because from 1990 to 2005, it housed both the Formation Year seminarians and the First Year Philosophy seminarians. With the adoption of the K-12 curriculum, a senior high school wing was added.

Discipleship Stage (Philosophy Department)

• Seminarians admitted to the First Year are only those coming from the Formation Year Department (or pre-college from other seminaries) and graduates of the minor seminary. During the four years of this stage, the seminarian is equipped with academic knowledge for critical thinking and understanding of matters of faith and morality, a profound sense of spirituality and community living, and grounding in pastoral activities.
• The Philosophy curriculum is compliant with the provisions of the Commission on Higher Education of the Department of Education. Seminarians who complete the academic requirements are granted the Bachelor of Arts (A.B.) Degree in Philosophy, Major in Classical Philosophy.
• The role of the Director can be equated with the term Prefect or Dean of Seminarians.

Configuration Stage (Theology Department)

• At this stage, the seminarian is formed to be a pastoral theologian in fulfillment of the demands of the church for his future ministry. He should exemplify traits of a responsible shepherd and conscious leader.
• There are five years allotted for the theological formation of a seminarian: 4 for the course proper and 1 for the PSIY. Between his Second Year and Third Year, he undergoes the Pastoral-Spiritual Integration Year (or PSIY) wherein he begins to discern seriously his vocation to the priesthood through lengthy activities of pastoral outreach, community building, and prayerful discernment.
• In the absence of the Seminary Rector, the Director of the Theology Department assumes the responsibilities of this post. In the past, there was a vice-rector who would assist in the key administration of the seminary. The last vice-rector, Estelito Villegas, was installed parish priest of Saints Peter and Paul Parish in Poblacion, Makati in January 2007, upon the request of the seminary fathers to cater the need for a seminary parish for the ongoing formation of seminarians.
• Seminarians who would complete the course requirements will be granted a Master's Degree in either Theology (thesis program), Pastoral Ministry (non-thesis), or Spirituality.
• The role of the Director can be equated with the term Prefect or Dean of Seminarians.

Directors of the Pastoral-Spiritual Integration Year

• 1992–1993, Celestino Pascual
• 1993–1994, Allen Aganon (Diocese of Parañaque)
• 1994–2000, Ronald Macale (Diocese of Cubao)
• 2000–2007, Estelito Villegas
• 2007–2015, Joselito Martin
• 2015-2023, Ramon Jade Licuanan
• 2023-present, Jaime Vidal Zuniga

The Pipe Organ of the Main Chapel of San Carlos Seminary.