The significant political and social events taking place at the end of the 18th Century and at the beginning of the 19th Century provoked important changes within the University itself, stimulating the reorganisation and the revision of its programmes of study.The University, once maintained and managed by local government institutions and protected by the Prince, was replaced during a new era of Papal monarchy that presided over the University. Under Papal authority, the University had limited administrative autonomy as its ruling bodies were directly controlled by the central Papal government in Rome. During this period, the University became a real centre of state culture.n the period immediately preceding 1860, the old Perugia Studium was rapidly reorganised, and transformed into a modern university. The first reforms were clearly manifestations of the revolutionary climate which existed at the end of the 18th Century. Among the promoters of these reforms were Hannibal Mariotti, Professor of Medical Theory and Anatomy, and perhaps the most representative figure of the political and academic world of that era; and Antonio Brizi, also a Professor at the University. After the Roman Republic experience and then a brief period of control by the Austrian government the University returned under Papal government.
The Papal government immediately provided a "Plan for the Re-opening of the University of Perugia" which included, the substitution of professors "affected by French views".
Despite this, the Anatomical-Surgical Academy, along with its surgical theatre was founded: a clear sign that the University was in touch with the new scientific progresses of the day, and the most modern and widespread ways of thinking and learning. With the union of the Papal States and Perugia to the French empire, decreed by Napoleon in May of 1809, new lines of authority reached the University.The advancements achieved during the Napoleonic period were so significant that the Papal government, reactivated by its reinstatement, decided not to bring about any administrative or academic changes, at least at first, while waiting for a new definite statute. This statute came only with Pope Leo XII, in August 1824: a single law that regulated every aspect of university life and applied to all the State's universities. The other episodes during the events that led up to national unity, in 1861, restored the city with an institution ready to grow and to create an environment in which research and teaching would re-bloom. This is evidenced by the establishment of the "Foundation for Agrarian Education" in 1892 and the "Institute of Experimental Agriculture", whose objective was to promote the advancement of agriculture through general research and the education of farmers.