Miguel de Benavides, who had come to the Philippines with the first Dominican mission in 1587, had gone on to become bishop of Nueva Segovia, and had been named archbishop of Manila in 1601.

Upon Benavides’ death in July 1605, he had bequeathed his library and personal property worth 1,500 pesos to be used as the seed fund for the establishment of an institution of higher learning.

Fr. Bernardo de Santa Catalina had carried out Benavides’ wishes and was able to secure a building near the Dominican church and convent in Intramuros for the College.

Permission to open the College had been requested in 1609 from King Philip III of Spain; this only reached Manila in 1611.

The Colegio de Nuestra Señora del Santísimo Rosario is established on April 28, 1611.

Later renamed Colegio de Santo Tomás, it will be elevated by Pope Innocent X to a university on November 20, 1645.

This makes the university the second royal and pontifical institution in the Philippines, after the Jesuit's Universidad de San Ignacio, which had been founded in 1590 but will be closed in 1768 following the expulsion of the Society of Jesus from the Philippines.