Ateneo de Zamboanga began as a parochial elementary school called Escuela Catolica in 1912, became a high school in 1930, and a college in 1952. It added a graduate school in 1976. It was started by Spanish Jesuit Fathers who were then in charge of the Immaculate Conception Cathedral, the Spanish church of Zamboanga City. Fr. Manuel Sauras ran the school while Fr. Miguel Sadera Mata was the pastor of the parish church.
In 1916, permission from Manila was given to the school to use the name Ateneo de Zamboanga, although it was still attached to the parish. The American Jesuits took over the administration of the school from the Spanish Jesuits in 1930. Two years later, the school became a recognized high school, but by then, it already turned out its first batch of high school graduates.
In 1946, the school became officially recognized as a Jesuit-run institution, under the jurisdiction of the Jesuit superiors and no longer attached to the parish.
The grade school started accepting girls in 1984. In 1992, the first batch of girls completed their elementary education.
To cater to the needs of the growing population, the grade school went through several phases of facility improvement. In 1994, the construction of the new building facing the Berchmans Hall began. This building houses the Grade School Library, Audio Visual Room. Science Laboratory, Computer Laboratories on the ground floor and six classrooms on the second floor. In 2000 the construction of the Kostka Hall was completed. This building houses eighteen (18) classrooms. The transfer of the high school to Fr. William H. Kreutz S.J. Campus in Tumaga in 2006, has allowed the grade school to have more space for the offices of the principal, the registrat and the school chaplain in the groundfloor of the Campion Hall and the additional of the wider audio-visual room in the second floor of the same hall.
In 1994, computer education was included in the curricular offerings of the grade school. This was first offered in Grade V & VI. Eventually, in 1997, the program was expanded and was offered to all grade school students.
The grade school was first granted a three year accreditation by the Philippine Accrediting Association of Schools, Colleges and Universities (PAASCU) in 1995. It was awarded a five year reaccreditations by the same agency in 1999 and in 2004.
In August 2001, the Ateneo de Zamboanga became University.