It was founded on February 1, 1950, by a group of prominent professors and intellectuals in response to the intolerance and political persecution that existed in the country, with the goal of creating a secular and welcoming institution apart from the political ideologies of the time.

In 2021, the National Ministry of Education renewed the university's Institutional Accreditation of High Quality until 2027.

In 2015, the university was involved in a scandal for the election of comptroller general of Antioquia in which Julián Bedoya, then the representative of the Chamber and ex-president of the Assembly of Antioquia, and Orfa Nelly Henao, president of the Assembly, had adjusted the convocation to choose the departamental comptroller so that the post would be given to professor Carlos Molina, given that the requirements were written with the help of said professor and included various requirements that only favored himself, such as holding a doctorate from a university abroad.

[6] In 2019, both the rector Néstor Hincapié and councilwoman Aura Marleny supported the candidate of David Ospina to occupy the post of comptroller of Antioquia, but his election was rejected by the city councils for fear that he had used his privilege to obtain election to this office.

[7] The rectorship of Néstor Hincapié ended in 2020 in a political scandal when the district attorney pressed criminal charges against the then-rector and various professors for having apparently given Julian Bedoya, who had not fulfilled the lawful requirements, a law degree in exchange for votes in favor of the university's political group.