As a state University, the Faculty of Medicine falls under the remit of the Ministry of Education and is accredited by both the Government of the Slovak Republic and the European Union. The university has adjusted to the Bologna Process and introduced the European Credit Transfer System (ECTS) in 2001. ECTS promotes the mobility of European students, making it easier for students to study abroad and to transfer their academic record to another university.

The University has been offering degree programmes in English for international students for over 15 years.

The University cooperates with other universities and European institutions in cities such as Prague, Paris, Nantes, Bordeaux, Padua, Essen, Düsseldorf, Amsterdam, Utrecht, Zurich, Salamanca and Krakow.

It also has ERASMUS agreements with a number of European universities, including the Faculties of Medicine of the University of Salamanca, the University of Málaga and the University of Miguel Hernández in Alicante.

The University has been a member of the European University Association (EUA) since 2004.

The European University Association is the representative organisation of European universities and national rectors conferences, and is the main voice of the higher education community in Europe. The EUA’s mission is to promote the development of a coherent system of European higher education and research within the EU. It aims to achieve this through the active support and guidance of its members to enhance the quality of education, learning and research and to contribute to the European community.

The Pavol Josef Safárik University is a signatory to the Magna Charta Universitatum.