In 1940, at the invitation of Bishop (later Archbishop) Pedro P. Santos of Caceres, the Ateneo de Naga was founded as a Jesuit school for boys, with Fr. Francis D. Burns, S.J. as the Rector. The classes were first held in the building formerly used by the Camarines Sur Catholic academy (now the Naga Parochial School). Meanwhile the construction of the new school building, dominated by the now well-known facade of four pillars, began. In December 1941 the small band of Jesuit moved to their new residence on campus and were preparing to transfer classes to the newly finished structures after the Christmas holidays, when suddenly on 8 December the Pacific War broke out.

When the Japanese Imperial Forces came to Naga, they imprisoned the Jesuits (except Bro. Sergio Adriatico, S.J., the lone Filipino among them), occupied the Ateneo de Naga, and converted it into the local Fort Santiago. As soon as Philippine independence was restored in 1946, the high school classes were resumed.

On 1 June 1947 the Ateneo de Naga was granted by the Department of Education full recognition as a standard four-year high school. On 5 June 1947 the College was opened with 87 male student. On 26 October 1953 the Ateneo College became coeducational with the admission of five women.

The steady growth of the Ateneo called for new structures for governance. Thus the 1940 Articles of Incorporation were amended and new By-laws adopted in 1979, transferring the school's highest governing authority to the Board of Trustees, majority of whom have been Jesuits.

Through its more than half a century of existence, the Ateneo has made significant breakthroughs and has suffered serious setbacks. Economic difficulties during the Martial Law years led to a dip in the college enrollment. But as the school marked its Golden Jubilee in 1990, there began a remarkable turn-around and recovery. The Graduate School, which had had a brief existence in the seventies, was revived in 1993.

In 1979, the College and the HIgh School were the first in Camarines Sur to be accredited by the Philippine Accrediting Association of Schools, Colleges, and Universities (PAASCU). They were accredited for the third time in 1992. In 1991 the Department of Education, Culture, and Sports placed the Ateneo in its list of 18 excellent universities and colleges in the country.

The 90s was a decade of development. The Ateneo implemented CORPLAN 2000. A vigorous faculty development program enabled faculty members to earn graduate degrees. An endownment Fund was establishment for scholarships and professorial chairs. Standards were upgraded. New courses were offered. Centers and institutes were established. New buildings were constructed. Enrollment increased. In 1997 the college was broken into four colleges: Arts and Sciences, Commerce, Education, and Information Technology and Engineering. 

On February 20, 1999 the Commission on Higher Education conferred the Ateneo de Naga, with the late Fr. Raul J. Bonoan, S.J. as the first university president. 

Last August 28, 1999 Fr. Joel E. Tabora, S.J. was installed as the second university president.