The University was founded on January 8, 1827 as the Oaxacan Institute for Arts and Sciences. Initially courses were offered in Medicine, Surgery, Civil and Natural Law, Public Law, Canon Law and Ecclesiastical History, Political Economy, Statistics, Geography and Physics, Mathematics logic, ethics, English and French.
In May 2006, a teachers' strike began in the Zócalo in the Mexican city of Oaxaca, Oaxaca. 2006 was the 25th consecutive year that Oaxaca's teachers have striked. Previously, the protests had generally lasted for one to two weeks and had resulted in small raises for teachers. 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. A street battle lasted for several hours that day, resulting in more than one hundred hospitalizations but no fatalities. Ortiz declared that he would not resign.
On November 2, 2006, Federal Preventative Police advanced on the University, occupied by students and displaced protesters from the Zocalo. Since the University is autonomous, the police are forbidden from entering the grounds, unless invited by the Rector .
Thousands of protesters arrived in the following hours, surrounding the police and eventually forcing them to withdraw from the area surrounding the university. The Asamblea Popular de los Pueblos de Oaxaca had received permission by the university rector to broadcast their messages through the university radio, which they used to criticise political parties, the Institutional Revolutionary Party specifically. Opinions against the APPO were quickly taken off the air
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 and that a tentative operation by the Federal Police would not be a solution to the issue
In 2001, the UABJO's School of Languages initiated a study abroad exchange program with the College of the Mainland, in Texas City, Texas, USA. This has led to increased exposure for the university as well as helped to further the mission of university's School of Languages.
Several prominent figures in the political life of Mexico have been alumni of UABJO and its predecessor, the Oaxacan Arts and Science Institute: