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.
The University of Évora was inaugurated on November 1st, 1559, as the University of Espírito Santo. It was handed over to the Society of Jesus, which ran it for two centuries.
The prestige of the University of Évora during the two centuries of its first phase of existence was confused with the prestige and scientific value of its professors. Relevant names of Portuguese and Spanish culture were attached to it.
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.