Founded in 1912 by Jesuits as Escuela Catolica, an all-boys parochial school of the Immaculate Conception parish, it is the second oldest Jesuit-administered institution in the Philippines.

In 1912, a parochial elementary school of the Immaculate Conception parish was opened by the Spanish Jesuits and named the Escuela Catolica.

An annual subsidy of ₱1,000, along with one-fourth of the diocesan revenue, the parish rectory, and financial support from the Catholic Action and various sources, were offered for the new school.

Francisco X. Tena, S.J., the Escuela Catolica was renamed to the "Ateneo Elementary School" on October 28, 1916[9] with seven grade levels.

Thomas returned to Zamboanga after being assigned elsewhere, he became the first American director of the school, which was granted by George C. Butte, the Secretary of Public Instruction, and approved by W.G.M.

[3]High school classes were held at the third floor of the Mindanao Theater building, previously purchased by the Knights of Columbus (K of C).

The high school was officially recognized by the city government in 1932, and the first graduates were produced in the same year, with Roseller T. Lim as the valedictorian.

[4] On February 13, 1946, a letter to the Jesuit Mission Superior was sent by Bishop Luis Del Rosario, urging the reopening of Ateneo to "counteract possible Protestant activities.

"[8] High school and intermediate classes were reopened in July 1946[6][10] and were held in a nipa-sawali building on the new site purchased by Fr.

The Philippine Coconut Producers Federation, Inc. (COCOFED) sponsored a new Bellarmine-Campion building for the high school, and construction was completed in 1979.

[7] In 1987, the Learning Resource Center was constructed through a grant from the United States Agency for International Development (USAID).

[6] Discussions were held in 1990 between health professionals and community leaders regarding the need for a medical school in Western Mindanao due to the region having the highest infant mortality rate in the Philippines at the time, among other factors.

William H. Kreutz, S.J., the university president during this time, established the Zamboanga Medical School Foundation, Inc. (ZMSF) as a non-stock, non-profit organization in 1991.

William H. Kreutz, S.J., in honor of the university president at the time, started construction in Barangay Tumaga on July 30, 2005, for the basic education units.

A certificate of authority was issued on May 18, 2011, and the Xavier University College of Law – Zamboanga opened in June 2011.

Legal Education Board members later granted Ateneo a permit to open a law school through an order dated January 13, 2014.

[25] On July 7, 2016, the historic 67-year-old Brebeuf Gymnasium was burned to the ground;[26] the Sauras, Kostka, and Gonzaga Halls were also damaged.

[31][32] In 2022, as the COVID-19 pandemic saw less cases during the year, it was returned to Ateneo from the city government and reopened on October 10, 2022, with future renovations planned for the campus.

[40] They are also active in community initiatives, such as organizing relief operations during the 2013 Zamboanga City Siege[41] and protesting against the implementation of mandatory Reserve Officers' Training Corps in the Philippines.

[42] Ateneo is governed as a private, nonprofit corporation by a board of trustees responsible for overseeing the long-term interests of the university.

Efforts were made by the Jesuits to incorporate Ateneo and establish a board of trustees, and on February 25, 1979, Fr.