The appointment to the post of Chancellor of the University of Lisbon (1959-62) gave Marcelo Caetano a more direct handling of issues related to university education. As the Chancellor, he headed the official Portuguese delegation to the Fourth International Colloquium on Luso-Brazilian Studies, held in Bahia, Brazil, where he returned to an issue that was already well-known to him: "Frei Serafim de Freitas and the controversy of the freedom of the seas." As Chancellor he sought to create a university environment across the different faculties. He can also be attributed with the promotion and administration of the first university holiday courses in Angola and Mozambique. In 1961 he inaugurated the current building of the Chancellor's Office of the University of Lisbon, with the Schools of Law and Literature already constructed. He continued his historical research. One example was his study on the Law School itself, Apontamentos para a História da Faculdade de Direito de Lisboa (Notes on the History of the Lisbon School of Law, 1960) – an essential reference for a historical perspective on the professors, staff and legislation, among other aspects, on the University of Lisbon School of Law, from its founding in 1913 until 1953. To this day, it is one of the few works on the School. Marcelo Caetano's involvement as Chancellor in a controversy with the University of Coimbra over the antiquity of the University of Lisbon should also be noted. The entire situation created enormous friction between the University Senates of both Universities, to the point that the Senate of the University of Coimbra stated that there was an "attempt to falsify historical truth" by the Senate of the University of Lisbon (Pela Universidade de Lisboa, 1974, pp. 65-93).

After the end of the 1962 academic crisis, in which he resigned as Rector due to disagreements with the Minister of Education, Lopes de Almeida, Marcelo Caetano (who sided with the students..) chose to move away from political life. He returned in 1968, succeeding Oliveira Salazar in the Presidency of the Council. The academic crisis may have ended up strengthening a certain more reformist and "liberal" image for Cataeno, in addition to his previous criticism of Salazar. His five-year break from active politics allowed him to return to the "refuge" of teaching and intellectual work, turning back to themes related to the colonies, medieval courts and Portuguese legal history. Evidence of latter was his Lições de História do Direito Português (Lessons in Portuguese Legal History, 1962; he left the chair of this department the following year), in which one observes an evolution from his textbook published 1941, in particular deeper analysis, at the expense of scope (Marcelo Caetano, historiador, p. 14).

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