Although the original idea of the creation of the second university of the Kingdom, belonged to D. João III, it was up to Cardinal D. Henrique, future king of Portugal, its realization.
With the consent of Pope Paul IV, expressed in the Bull Cum a nobis April 1559, the new University was created, with the right to teach Philosophy, Moral, Scripture, Speculative Theology, Rhetoric and Humanities, which fully inserts this University within the framework. traditional counter-reformist of the European Catholic institutions of higher education, most of which are controlled by the Jesuits. It could not, however, be teached Medicine, Civil Law and the contentious part of Canon Law. In the reign of D. Pedro II, the teaching of Mathematics would be introduced, covering such varied subjects as Geography, Physics, or Military Architecture.
A Universidade de Évora foi inaugurada a 1 de Novembro de 1559, como Universidade do Espírito Santo. Foi entregue à Companhia de Jesus, que a dirigiu durante dois séculos.
O prestígio da Universidade de Évora durante os dois séculos da sua primeira fase de existência confundiu-se com o prestígio e o valor científico dos seus docentes. A ela estiveram ligados nomes relevantes da cultura portuguesa e espanhola.
In 1759 it was closed by order of the Marquis of Pombal, when the Jesuits were expelled. It was eventually closed.
From the second half of the nineteenth century, the noble Henriquino building was installed the Lyceum of Évora, to which Queen Dona Maria II granted the prerogative of the use of "cape and cassock", ", in attention to the universityt radition of the city and the building.
In 1973, by decree of the then Minister of Education, José Veiga Simão, the University Institute of Évora was created, which was to become extinct in 1979, to make way for the new University of Évora.