The beginnings of the Faculty of Medicine go back to 1364, when King Kazimierz the Great founded the Academy of Kraków, which initially consisted of three faculties: law, medicine and philosophy. Throughout history the Faculty of Medicine was a part of the university but in 1950 due to political reasons all faculties of medicine in Poland were transformed into separate institutions, known as medical academies.

Although the Medical Academy of Kraków earned a high reputation, a strong wish to become a part of the Jagiellonian University again was very much alive. The wish became reality when the Faculty returned to the Jagiellonian University on May 12, 1993.