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 Rector. It was registered with the SEC on May 2, 1940 as a non-stock, non profit educational institution.
On June 1, 1947 the Ateneo de Naga was granted by the Department of Education full recognition as a standard four-year high school. On June 5, 1947 the College was opened with 87 male students. Six years later, on October 26, 1953, The Ateneo College became coeducational with the admission of 5 women.
The University status was granted to the Ateneo de Naga on November 11, 1998 upon the approval by the Commission on Higher Education of Resolution No. 142-98. Its conferment and the installation of the first University President, Fr. Bonoan was celebrated on February 20, 1999.
In 2008, it became the only University in Southern Luzon to be granted by CHED with Autonomous Status. ADNU has the most Centers of Development: in Information Technology, Business Administration and Entrepreneurship; and Center of Excellence in Teacher Training in the region.
In 2009, it was one of the three universities in the country to obtain Institutional Accreditation from PAASCU.