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The  Ateneo de Zamboanga University began in 1912 as Escuela Catolica, a parochial school run by Spanish Jesuits at the old site of the Immaculate Conception Church right across the Sunken Garden.  Fr. Manuel M. Sauras, S.J. was the first director.

In 1916, the Escuela Catolica became the Ateneo de Zamboanga.  In 1930, the American Jesuits took over the Spanish Jesuits with Fr. Thomas J. Murray, S.J. as the first American director.  Classes were held in the Knights of Columbus ( K of C ) building, now the site for the City Theater.  The first high school students graduated from Ateneo in 1932.

In 1938, a library was built on the first floor of the K of C Building.  A façade, an auditorium, and an annex were also built. John Shinn was appointed headmaster of the Grade School and Fr. Francis X. Clark, S.J. became the principal and dean of discipline of the High School Department.  The school was closed during World War II.  It was used by the Japanese as a public school until it was shelled and bombed by American forces on March 8 and 9 in 1945, prior to the liberation of the city.

The high school reopened in 1946, with a nipa-sawali building on a new site outside of the poblacion called the Jardin de Chino near Camino Nuevo.  It was providential that shortly before the outbreak of the war, Fr. Eusebio G. Salvador, S.J. had bought 18 adjoining lots in that section.

In 1948, the school was officially recognized as a Jesuit school apart from the parish. The post liberation years were a period of rapid physical, curricular, and enrollment expansion of the school.  A college was established in 1952 and a graduate school in 1976.  Later in 1994, the Zamboanga Medical School Foundation was established and entered into consortium with the Ateneo at the La Purisima campus.

The Commission on Higher Education granted University Status to the Ateneo de Zamboanga on August 20, 2001.
In July 31, 2005 a groundbreaking for the new high school site was undertaken. This is located in Savanah, Tumaga, Zamboanga City.
On school year 2006 – 2007, the whole High School community is moved to the new site.