Public university schools have a long history in Portugal. They started in the Middle Ages, and like other European medieval universities at the time, they were founded by the monarchs under the authority and supervision of the Catholic Church. For many centuries there was only one university, the University of Coimbra, founded in 1290 in Lisbon. It was founded as a Studium Generale (Estudo Geral). Scientiae thesaurus mirabilis, the royal charter announcing the institution of the current University of Coimbra was dated 1 March of that year, although efforts had been made at least since 1288 to create this first university studies in Portugal. Throughout history it transferred between Coimbra and Lisbon several times, definitely settling in Coimbra during the 16th century (1537). The Colégio do Espírito Santo, a university college, was an old higher learning institution which operated between 1559 and 1759 in Évora, but it was shut down during the Marquis of Pombal government, because it was run by the Jesuits, and the marquis implemented strong secular policies. A new state-run university at Évora was founded in 1973 - the University of Évora. Within the scope of the Portuguese Empire, the Portuguese founded in 1792 the oldest engineering school of Latin America (the Real Academia de Artilharia, Fortificação e Desenho), as well as the oldest medical college of Asia (the Goa Medical College) in 1842.
Since the population was largely illiterate, the two universities at Coimbra and Évora, and some later higher-education schools in Lisbon (e.g. (Escola Politécnica: 1837-1911; Curso Superior de Letras: 1859-1911; and Curso Superior de Comércio: 1884-1911)) and Porto (successively Aula Náutica: 1762-1803; Real Academia da Marinha e Comércio: 1803-1837; and the Academia Politécnica: 1837-1911), were enough for a small population inside a territory like Continental Portugal of the 16th-19th centuries. During the 19th century some other isolated higher-education schools were established. For instance, two medical schools were established: the Lisbon Royal Medical-Surgical School and Porto Royal Medical-Surgical School opened in 1825. They were later incorporated into two new universities created in 1911 in Lisbon and Porto, which also absorbed Lisbon's former Escola Politécnica and Curso Superior de Letras, and Porto's Academia Politécnica, which were reformed and upgraded their facilities in the same year. Other successive institutions were the IST - Instituto Superior Técnico and the Instituto Superior de Comércio, successor of the former Curso Superior de Comércio, (today ISEG - Instituto Superior de Economia e Gestão), both born from the former Lisbon Institute of Industry and Commerce which originated the creation of university schools in 1911.
With the advent of the Republic, the University of Lisbon and the University of Porto were created in 1911. In 1930, a new university in Lisbon was created, the Technical University of Lisbon, which incorporated the Instituto Superior Técnico and some other university institutes and colleges such as the Instituto Superior de Comércio, and agriculture and veterinary schools.
In 1972 the ISCTE, a public university institute, was created in Lisbon by the decree Decreto-Lei nº 522/72, of 15 December, as a first step towards a new and innovative public university in the city. Due to the carnation revolution of 1974 this first facility of a never-completed projected larger university stayed alone. In 1973 a new wave of state-run universities opened in Lisbon - the New University of Lisbon, Braga - the Minho University and Évora - the University of Évora. These last days of the Estado Novo regime were marked by the most significant growth in enrolments for both secondary and university education in Portugal. After 1974, the anti-Estado Novo revolution's year, new public universities were created in Vila Real - the University of Trás-os-Montes and Alto Douro, Aveiro - the University of Aveiro, Covilhã - the University of Beira Interior (upgraded from the former Polytechnic Institute of Covilhã which was created in 1973), Faro - the University of the Algarve, Madeira - the University of Madeira, and the Azores - the University of the Azores.
In 1988, the Portuguese government founded a public distance university, the Universidade Aberta (Aberta University), an "Open University" with headquarters in Lisbon, regional branches in Porto and Coimbra, and study centres all over the country.
In the 1980s and 1990s, a boom of private institutions was experienced and many private universities started to open. Most private universities had a poor reputation and were known for making it easy for students to enter and also to get high grades. In 2007, several of those private institutions or their heirs, were investigated and faced compulsory closing (for example, the infamous Independente University closing) or official criticism with recommendations that the state-managed investigation proposed for improving their quality and avoid termination.
Without large endowments like those received, for example, by many US private universities and colleges which are attractive to the best researchers and students, the private higher education institutions of Portugal, with a few exceptions, do not have neither the financial support nor the academic profile to reach the highest teaching and research standards of the top Portuguese public universities. In addition, the private universities have faced a restrictive lack of collaboration with the major enterprises which, however, have developed fruitful relationships with many public higher education institutions.
Nowadays, the Catholic University of Portugal, a private university with branches in the cities of Lisbon, Porto, Braga, Viseu, and Figueira da Foz (founded before the others, in 1967, and officially recognized in 1971), offers some well-recognized degrees. This private university has a unique status, being run by the Catholic Church.
The Portuguese universities have been the exclusive granters of master's and doctoral degrees in the country and are to this day the major source of research and development in Portugal. Today, as in the past, they have full autonomy to offer all levels of academic degrees and the power to create new graduate or undergraduate courses in almost every major field of study. By the time of the implementation of the Bologna Process (2006) in Portuguese higher education, 42.5% of the state-run university teaching staff had a doctorate degree in 2005 - 65% in 2007 after the Bologna Process.
Due to the Portuguese sovereign debt crisis in the late 2000s, and the subsequent IMF-EU financial assistance to the Portuguese Republic from 2011 onward, many universities and other higher education institutions suffered financially. Many were on verge of bankruptcy and were forced to increase its admissions and tuition fees while the budget dwindled and staff members and bonuses were being reduced.