[2] Its first antecedent dates from August 26, 1825, as the Institute of Sciences and Arts of Oaxaca under the decree of the then governor Ignacio Morales, with the protection of the local congress, but it was not until January 1827 that it opened its doors on San Nicolás street, today Independencia Avenue, being Fray Francisco de Aparicio, a priest of liberal ideas, its first rector.

In 1845 the institute stopped offering the ecclesiastical career and favored that of law and medicine, later creating that of Political Economy.

The 2006 strike began in protest of the low funding for teachers and rural schools in the state, but was prompted to additionally call for the resignation of the state governor Ulises Ruiz Ortiz after 3000 police were sent to break up the occupation in the early morning of June 14, 2006.

On November 2, 2006, Federal Preventative Police advanced on the university, occupied by students and displaced protesters from the Zocalo.

Opinions against the APPO were quickly taken off the air [4] After criticism by the private sector, political organizations and the press (specifically Grupo Formula's news anchor Denise Maerker) for his remarks towards the APPO the rector declared that he had requested respect for the rights of students and faculty [5] and that an operational attempt by the Federal Police would not provide a solution to the issue [6] The Faculty of Languages at Benito Juárez Autonomous University of Oaxaca is a major focus of the university's scholarship with campuses in Oaxaca City, Tehuantepec and Puerto Escondido.