The school was founded by the late Rodolfo Neri- Pelaez of Cagayan de Oro City and his wife Elsa Pelaez of Cebu City. The institution got its University level 111 status in 1998 from the Commission on Higher Education in 2003. Dr. Rafaelita P. Golez served as President of the university.

During its first 25 years, Liceo de Cagayan University was a tertiary – level institution offering courses in law, commerce, engineering and liberal arts. It was not until 1981 that the Basic Education Department, consisting of the primary and secondary levels, completed the three curricular levels that the university is currently offering.

The university offers courses in Nursing, Physical Therapy, Radiologic Technology, Computer Engineering, Electronic and Communications Engineering, Tourism and Computer Information Systems. In 1998, the university became the first in the country to offer a graduate pogram, the Diploma / Master of Local Governance Scholarship Program funded by the Canadian government and Civil Service Commission. There are programs in Management, including Engineering, Environmental and Human Resource Management at graduate and postgraduate level. The university also offers Information Technology courses.