The University of Évora was the second university to be established in Portugal. After the founding of the University of Coimbra in 1537, the need for another university to serve the South of the country was felt. Évora, ecclesiastical metropolis and temporary residence of the Court, immediately emerged as the most suitable city. Although the original idea of creating the second university of the Kingdom belonged to D. João III, its implementation has fallen to Cardinal D. Henrique. Interested in teaching issues, he began by founding the College of the Holy Spirit (Colégio do Espírito Santo), entrusting it to the newly founded Society of Jesus (Companhia de Jesus).
When the work on the building was still underway, the Cardinal asked Rome to transform the College into a full University. With the consent of Pope Paul IV, expressed in the Bull Cum nobis of April 1559, the new University was created, with the right to teach all subjects, except Medicine, Civil Law and the contentious part of the Canon Law. The solemn inauguration took place on November 1 of that same year. Even today, the University's anniversary is celebrated with the solemn opening ceremony of the academic year.
The main subjects taught were Philosophy, Morality, Scripture, Speculative Theology, Rhetoric, Grammar and Humanities, which fully inserts this University in the traditional counter-reformist framework of European Catholic institutions of higher education, much of which, in fact, controlled by the Jesuits.
During the reign of D. Pedro II was introduced the teaching of Mathematics, covering subjects as varied as Geography, Physics, or Military Architecture. Along the two centuries of its first phase of existence, the prestige of the University of Évora was confused with the prestige and scientific value of its professors. Relevant names of Portuguese and Spanish culture were linked to it, of which it is important to highlight, first and foremost, Luis de Molina, theologian and moralist of creativity and European reputation. In Évora, another luminary of the Iberian culture of that time, the Jesuit Francisco Suárez, who was later a professor at the University of Coimbra, received his doctorate. Here also taught Pedro da Fonseca for some time, considered the most important Portuguese philosopher from the 16th century, famous for his effort to renew neo-scholasticism in Aristotelian thought.
Despite the attempts to modernize and open up the new scientific spirit characterizing the University 17th century, it must be recognized that, like happened with its elder sister in Coimbra, the effort did not translate into actual opening of minds to the needs of the new times. Notwithstanding the high individual value of many teachers, the broader education system proved to be misfit and outdated. Thus, Évora participated in the global trend of turning back to Transpirenaica Europe that characterized the majority of elites and Iberian cultural institutions of the Old Regime.
Not surprisingly, when the political and cultural conjuncture of the mid-18th century began to prove hostile to the Jesuits, the University of Évora had easily become a target of the reform and centralist policy of Pombal. On February 8, 1759 - two hundred years after its foundation - the University was surrounded by cavalry troops, as a result of the decree to expel and ban the Jesuits. After a long time of seclusion under arms, the masters were eventually taken to Lisbon, where many were imprisoned in the sadly celebrated Fort of Junqueira. Others were summarily deported to the Pontifical States.
Since the second half of the 19th century, the Lycée of Évora was installed in the noble henriquine building, to which Queen Dona Maria II granted the prerogative of the use of "cloak and cassock", regarding the city and building´s university tradition.
In 1973, by decree of the then Minister of Education, José Veiga Simão, the University Institute of Évora was created, which was extinct in 1979 to give place to the new University of Évora.