The Don Bosco Salesian Association signed an Academic Cooperation Agreement with the Francisco Marroquín University in 1971. Starting in 1972, the Don Bosco Salesians developed humanistic programs supported by the Francisco Marroquín University. Careers, departments, and faculties were created. Notable among these programs are: Teachers in Education and Education Sciences, Teachers in Theology, Teachers in English, and Teachers in History. The Faculty of Communication Sciences had great development and the specialties of Technician and Bachelor of Science in Social Communication, Bachelor of Advertising and Bachelor of Radio and Television Production were established. There the Mesoamerican University had its beginnings.
Taking advantage of the university experience and development that had been achieved, the procedures for founding a new university began in 1996. The 1st. In October 1999, the Mesoamerican University was approved by the Council of Higher Private Education of Guatemala. In 2000, the new university began to function with the Faculties of Human and Social Sciences and Social Communication Sciences. One year later, in a strategic alliance with the Guatemalan Association of Managers, ESAG, Escuela Superior de Alta Gerencia, was created to teach Master's Degrees. In 2002, 15 careers from the city of Quetzaltenango were merged as part of the Mesoamerican University. In 2003, the Faculty of Medicine was authorized at said headquarters.