At the request of Bishop Pedro P. Santos of the Diocese of Nueva Caceres, the Jesuits founded the Ateneo de Naga in 1940 with Fr. Francis D. Burns, SJ as Rector. The first classes were held in a building near the Cathedral while new buildings were still being constructed in a new site just 200 meters away.

Shortly before the summer of 1941, the first high school graduation was held at Los Baños Building (now Oyster Restaurant) with Fr. Miguel Selga, SJ of the famed Manila Observatory as guest speaker and Ramon Belleza as valedictorian. Few weeks after the Jesuits moved into their new residence, World War II broke out in December 1941 and the Japanese Imperial Forces used the new campus as a garrison and concentration camp. All the American Jesuits were imprisoned except for the lone Filipino Jesuit Brother, Sergio Adriatico. Throughout the duration of the war, the Ateneo became the dreaded Fort Santiago of Bikol.

High school classes resumed in July of 1946 and a year after, the college department was opened with 87 male students. Six years later, in 1953, the college became coeducational with the admission of the first five female students.

The sixties was a period of change. The worsening socio-economic problems called for every Christian to be responsible. The response of Jesuit schools was summed up in the watchword: SPES, latin word for hope, hope through a social-political-economic-spiritual renewal. It called for involvement. What followed was a time of restlessness and student activism, a time for demonstration and clamor for change. Around the four pillars, in the city streets, Ateneans joined their peers in denouncing injustices, whether by teachers in school, or by political leaders in the city and the nation.

The Society of Jesus was not spared the crisis. As Jesuit manpower began to drop sharply, a layman had to take over the reins of the high school for the first time in Ateneo’s history. Antonio T. Olin became the first lay principal.

Martial Law was declared on September 21, 1972. The school was held suspect as a breeding place for subversives. Yet as the New Society began to take roots, the Atenean seemed to take an indifferent, apathetic stance. The glory of victory in interscholastic competitions was no longer attractive as before; the honor and pride in personal achievements no longer drove one to the limits of one’s potentials. The quality of students declined. How to explain this? Perhaps it was because Ateneo itself was no longer clear whether the school should stand for excellence in academics and character formation or for social involvement and reaching out to the poor and the oppressed.

In early 1975, the Jesuits concluded their 32nd General Congregation in Rome. Clearly they defined their mission today: Promotion of justice in the service of the faith. The Jesuit Superior General, Fr. Pedro Arrupe, SJ, thus instructed his men to evaluate all their works in the light of this mission, draw up their priorities, and make their decisions. The new watchword was: Men and Women for Others.

In 1976, another layman, Sofronio Llorin, took over the reins of the high school. The high school conducted an institutional self-survey and after three years of hard work at self-improvement, received formal accreditation from the Philippine Accrediting Association of Schools, Colleges, and Universities (PAASCU) in 1978. The principal at this time was Gregorio Abonal.

In 1979, a year before its Ruby Anniversary, the first Board of Trustees was formed, holding the highest policy-making authority.

From 1972 until 1988 the school was beset with enormous financial and academic problems. While almost on the brink of closure, the appointment of Fr. Raul J. Bonoan, SJ in 1989 as the new Ateneo de Naga President quickly brought a turn around.

In 1990, as the Ateneo celebrated its Golden Jubilee, a multi-million pesos Golden Jubilee Endowment Fund was launched which provided scholarships to poor but deserving students. A portion of this fund was allocated for faculty development.

The grant of the USAID-ASHA for a science building in 1991 signaled the beginning of a sustained and vigorous physical development of the campus. This building was named in honor of Rev. John J. Phelan, SJ the longest serving Jesuit in Ateneo de Naga. In a span of five years, since the completion of the Phelan Hall, six more buildings were constructed.

The designation in 1992 by the Department of Education, Culture and Sports (DECS) of Ateneo de Naga as one of the 18 Excellent Colleges and Universities in the country likewise paved the way for the re-opening of the Graduate School. In 1997, aside from the Graduate School, the Ateneo expanded into four colleges, namely: the College of Arts and Sciences, Commerce, Education and the College of Information Technology and Engineering. On November 11, 1998, the Commission on Higher Education (CHED) granted the university status to the Ateneo de Naga.

On February 20, 1999, the formal inauguration of the Ateneo as a University was held and Fr. Raul J. Bonoan SJ was formally installed as the First University President.

Barely two months after its inauguration as a university, the Ateneo lost its first President. On July 31, 1999, Fr. Joel E. Tabora, SJ succeeded as the Second University President.

Today, the University continues in its growth and development. New buildings have sprung. To date, the new additions are: Xavier Hall, the Jesuit Residence, Arrupe Hall, Engineering Building, the University Church, and the Madrigal Hall. A new school complex in Pacol now houses the high school which became coeducational in school year 2003-2004.