It was established in 1945 when the Jesuits took over the administration of the diocesan secondary school, Cagayan Valley Atheneum.

Filipinos who identified the title "Ateneo" with Jesuit schools and who knew the Latin parent, if not the meaning, of the word, were surprised and even disturbed that a new school was opening in Northern Luzon under the title of Cagayan Valley Atheneum—not conducted by the Jesuits.

The Cagayan Valley Atheneum, a secondary school, was founded by Constancio Jurgens, bishop of Tuguegarao in 1938.

The school reopened in temporary structures of nipa and sawali erected in the patio of the pre-war compound.

Shortly after its reopening during the school year 1945–1946, the Atheneum was committed by Bishop Jurgens to the direction of the Society of Jesus, and prior to school year 1949–1950, complete jurisdiction was transferred to the Society, due to the withdrawal of the C.I.C.M.

Two buildings, Loyola and Xavier Halls, were completed in time for occupancy before the second semester of school year 1950–51.

A third building, Bellarmine Hall, was completed shortly after the beginning of the second semester and used for boarders' dining room.

Father Pascua is to be reckoned among the "noteworthy features" of the Ateneo de Tuguegarao, for he had been active in the school since the Jesuits first came in 1946.