It is the fifth oldest and the last seminary that was established during the Spanish colonial period in the Philippines.

On May 27, 1865, Pope Pius IX, in the bull of erection Qui Ab Initio of the Diocese of Jaro, insisted that a new bishop should found and organize a seminary as soon as possible.

At that time, Mariano Cuartero, the first Bishop of Jaro, was still in Spain, acting as General Procurator of the Dominican Order.

He received episcopal ordination at the Dominican Seminary of Ocania, Spain, in November 1867, and was able to take possession of his diocese only on April 25, 1868.

The new bishop founded the Diocesan Seminary where he could train good pastors for the different parishes, which at that time were almost entirely under the spiritual administration of the Augustinian friars, who were then regarded as the Fathers of the Faith in Panay.

On April 2, 1868, Cuartero arrived in Manila together with five Vincentian priests, three Brothers and sixteen Daughters of Charity.

Having taken possession of the diocese, Cuartero began his work immediately of enlarging the parish of "La Candelaria" to be his cathedral church, the adaptation of the convento to be his residence and the foundation of the Diocesan Seminary in December 1869.

The first Vincentian Fathers who took the direction of the Seminary of Jaro was made of three priests: Ildefonso Moral, rector, one of the greatest figures in the early history of the Vincentians in the Philippines; Aniceto Gonzales, who directed the construction of the seminary building and later, succeeded Moral as rector; and the newly ordained priest, Juan Miralda.

Before the end of 1870, two young priests, Juan Jayme and Rufino Martin and a brother of Francisco Lopez joined the community.

On March 11, 1871, the cornerstone was laid and the construction of the seminary begun under the direction of Aniceto Gonzales who acted as foreman.

The number of students who requested to be allowed to take secondary education in the seminary but without any intention of pursuing priesthood was so many.

Statistics found in the book "Exposicion General de las Islas Filipinas in Madrid, 1887-Memoria" show a total enrolment of 5,344 for the year 1875–1885.

Since the American soldiers occupied the seminary, the fathers made their residence in Colegio de San Jose.

The arrival of Bishop Frederick Zadok Rooker in the diocese helped a lot in reorganizing the seminary life.

His friends in America gave the funds spent for this improvements, which brought prosperity days to the seminary.

On the night of October 7, 1906, a sudden fire caused by a candle, left carelessly burning in the sacristy by the seminarian in charge of it, reduced the building into a heap of ashes.

The prosperous days brought about by the rebuilding of the seminary increased the yearly enrolment to 180 interns and around 600 externs.

[citation needed] This fact and the reason that the Seminario-colegios were not what the church meant them to be, moved the Pope to exert all the means available to restore the seminaries to their purpose.

Pope Leo XIII, for instance, wrote to the bishops in 1899: "It must not be forgotten that the only and exclusive purpose of the Seminary is the formation of the youth, not for civic careers, whatever good and noble they may be, but for Priesthood."

Theoretically the seminarians' tuition fee per semester was Php 80.00; many of them could not pay their accounts because they came from poor families.

In 1920, the arrival of Bishop James McCloskey in the Diocese of Jaro brought financial stability to the St. Vincent Ferrer Seminary.

The atmosphere became tense and Mariano Auzmendi, rector, caught by the general panic and perilous situation, closed classes on December 12.

Due to the fact that McCloskey was sick and hospitalized in Manila, the rector, after having obtained permission from the Japanese, took the ten ordinands to Bacolod for their priestly ordination on June 29.

Early in the morning a squadron of American planes appeared in the sky heading straight toward the seminary.

In less than thirty minutes the building, which was a lasting tribute to the American bishops, in favor of the Jaro Clergy became a pile of ashes and twisted irons.

Meanwhile, Bishop Jose Maria Cuenco was planning to put up a solid and more prestigious building than the one destroyed by the bombs.

On June 19, 1946, the Archdiocese of Jaro (Elevated; 1951) had again a modern and excellent feminary for the proper training of its future priests.

The number of seminarians had broken all the previous records, introducing new subjects and adding new courses and had updated the plan of studies.

In 1958, the St. Vincent Ferrer Seminary obtained government recognition of its studies of philosophy and power to grant the bachelor of arts degree.

The Saint Vincent Ferrer Seminary takes pride in having produced distinguished clergymen like Gabriel Reyes, the first Filipino Archbishop of Manila, and Cardinal Jaime Sin who also became the Archbishop of Manila and had inspired the People Power Revolution at EDSA that set off a wave of democratization movements that spread to Taiwan and South Korea and even fell the Berlin wall and ended Communist rule in Eastern Europe.