Before the Jesuits were expelled from all Spanish territories, their first Christian mission in the Philippines began in Butuan, which was a center for missionary activity from 1521 to the early 1600s.  Following a series of politically-driven decisions of Europe under the Bourbons, the Jesuits were slowly driven out of Spanish territories until the orders reached the Philippines in 1768.

On June 13, 1859, the Jesuits returned to the Philippines at the request of Queen Isabel II, the order for their expulsion having been repealed earlier in 1814.  The Governor General then retained some of the missionaries in Manila and they re-established Escuela Pia, which is now the Ateneo de Manila University.  Almost three years after setting foot on Philippine soil again, the Jesuits arrived at Tamontaca, Cotabato, which became their pioneering mission field in their new wave of evangelization. Throughout the following decades of their work, and  with the spread of Christianity in the island came Jesuit academic institutions that would become among the prestigious universities in the country.
Commemorating 400 years of the Jesuits in the Philippines, featuring Philippine hero Dr. José P. Rizal ; pioneering meteorologist and Director of the Manila Observatory Padre Federico Faura y Prat, S. J.; peacemaker on Mindanao and "Apostle of Agusan" Padre Saturnino Urios, S. J.; and Jesuit founder St. Ignacio López de Loyola
Fr Saturnino Urios, who spent 40 of his best years building Christian towns along the Agusan River, founded in 1901 a school in Butuan, which would later be named after him.  Although technically the first Jesuit school in Mindanao, it was a parochial school whose administration also changed when the Jesuit mission in the area was taken over by another order.  In 1912, the Jesuits opened the Escuela Catolica in the Zamboanga Peninsula, which later was renamed Ateneo de Zamboanga.

Ateneo de Cagayan opened in 1933 with the coming of the American Jesuits, specifically by order of Fr James TG Hayes who saw the need to establish secondary schools in what was then Cagayan de Misamis.  Although with a somewhat small population, Cagayan was becoming the center of trade and commerce in Northern Mindanao, which had the the finest port in the entire island. Cagayan was also conveniently near the Jesuit missions along the Pulangi River in Bukidnon and Rio Grande in Cotabato, with Ateneo de Davao established only in 1948.

With the Jesuits’ known excellence in pedagogical work, Ateneo de Cagayan offered in 1938 the Elementary Teachers, its first college program.

At first classes were held at a two-storey wooden building in Burgos Street. Later, the school transferred to its present campus along Corrales Street to accommodate more students, and new courses–Liberal Arts and Commerce–were offered.
However, the school was forced to close when World War II broke out.  Its chemistry laboratory was first used to extract quinine for the defense forces but later was taken over and used as headquarters of the Japanese in May 1942.  The worst devastation the school suffered, however, was when American liberator planes bombed Cagayan two years after, reducing the buildings to rubble.

Reconstruction was immediately undertaken after the war. Literally rebuilt from ashes and together with the economic recovery of Northern Mindanao, the school reclaimed its stature.  In 1958, under the direction of Fr Francisco Araneta, Ateneo de Cagayan was granted university status, becoming the only university in Mindanao at that time.  It was then renamed Xavier University after Fr. Araneta’s promise to St Francis Xavier that should the school be granted the status before the commencement exercises that year, it would be renamed in his honor.

Adhering to continue the paradigms it has set, Xavier University engages in researches and extension services to address the intellectual and spiritual needs of the people in its locality–Northern Mindanao and its neighboring regions.