It was established in 1940 when the Jesuits took over the administration of the diocesan school, Camarines Sur Catholic Academy.

The Ateneo de Naga University was established in 1940 when American Jesuits took over the Camarines Sur Catholic Academy, a small private school under the supervision of the Diocese of Nueva Caceres, at the invitation of Bishop (later Archbishop) Pedro P. Santos of Caceres.

Santos initiated the construction of the Jesuit faculty house and the now iconic Ateneo de Naga building with the four pillars.

The law school offers a four-year program leading to the Juris Doctor (JD) degree.

In the early 2000s, a ten-hectare land in Barangay Pacol, Naga City, was donated to AdNU.

With the availability of more land, Ateneo de Naga can now admit a bigger student population.

The pre-school facility (the Ateneo Child Learning Center) also moved to the Bonoan Campus by school year 2014–2015.

Senior High School (SHS) of the Ateneo de Naga University is housed at Bagumbayan Campus.

It has five (5) academic tracks: Arts and Design Track (AVFX); Accountancy, Business, and Management (ABM); General Academic Strand (GAS); Humanities and Social Sciences[1] (HUMSS) and; a unique Humanities and Social Sciences-Social Journalism (HUMSS-SJ).

In 2001, Ateneo de Naga was among the first 22 private higher education institutions in the Philippines granted by CHED deregulated status for five years.

[3] As of 2020, Ateneo de Naga is the only autonomous and institutionally accredited university in the Bicol region.