The Ateneo de Manila University traces its roots to 1859 when, at the request of the City of Manila endorsed by Governor Norzagaray, The Jesuits took over the "Escuela Municipal" in Intramuros (the Walled City of Manila). A primary school originally intended for the sons of Spaniards, it was opened by the Jesuits to native Filipinos as well. In 1865 the Jesuits received government approval to add a five-year program leading to the degree of Bachelor of Arts.

In keeping with its academic status, the school was renamed "Ateneo Municipal de Manila." Courses in music and arts were also taught, and subsequently technical courses were added leading to the certificates in Agriculture, Surveying and Business. Among the graduates in those early decades was Jose Rizal, A.B. 1877.

At the turn of the century the new American regime brought about many changes in the Ateneo. In 1901 with the withdrawal of city subsidy, the Ateneo became a private institution dropping the word "municipal" from its official title. In 1921 the American Jesuits of the Maryland-New York Province replaced the Spanish Jesuits as teachers and administrators of the Ateneo.

The Intramuros fire of 1932 completely destroyed the Ateneo buildings, forcing the school to move to a new location in Padre Faura, Ermita. During the Battle of the Liberation of Manila, the Padre Faura complex of building was razed to the ground. Temporary structures were quickly built, and with the help of funds solicited locally and from abroad, the Ateneo moved to its present sprawling campus in Loyola Heights, Quezon City. In 1958 the Jesuits in the Philippines were constituted a new Province independent of the New York Province. Thus administration of the Ateneo passed on to the Philippine Province of the Society of Jesus and shortly after, its first Filipino president and rector was named. The growth of Ateneo demanded a new status and in 1959 the school obtained its university charter.

The Ateneo de Manila University today comprises the following academic units: the School of Arts and Sciences, the Graduate School of Business, the College of Law and the Ateneo Computer Technology Center (ACTC). In addition, like most Philippine universities, it runs a high school and grade school, noted for their high educational standards. The following social research and social development institutes, viz. Institute of Philippine Culture (IPC), Human Resources Center (HRC), Center for Community Services (CCS), Center for Social Policy and Public Affairs (CSPPA) constitute the Social Development Complex. Also located at the Loyola Heights campus are the Central Guidance Bureau, Manila Observatory, the Loyola School of Theology, San Jose Seminary and the East Asian Pastoral Institute.

The Ateneo de Manila is the oldest of the Philippine Ateneo schools.