The National University of Itapua was founded in 1996. Established by law No. 1009 dated on December 3, 1996. The proposal was submitted on March 25, 1995 to the Paraguayan Congress by Lorenzo Zacarías López who was the chair committee.
On June 24, 1995 a Central Coordinating Committee was conformed by departmental representatives, local authorities, educators, politicians, businessmen and professionals from the city of Encarnacion. On November 7, 1996, the Board of Universities resolves the creation and the start up of UNI with the openings of two careers, Medicine and Electromechanical Engineering.