The first Chairs of Pharmacy in Poland were formed as a direct result of the disbanding of the Jesuit order in 1773. At the time, this order had complete control over the entire Polish education system. The fact that the Commission of National Education was able to take over Jesuit possessions made education reform all the more possible. The end result was a three-stage secular educational system with elementary schools at the base and two universities (or Main Schools, as they were called) - the Crown School of Kraków and the Lithuanian School of Vilnius - at the top.
Andrzej Badurski was the major initiator of reform in the teaching of pharmacy. Andrzej Szaser also helped in implementing these reforms. In 1783, the Chair of Pharmacy and Medical Matter was established at the Crown School of Kraków. Its first Professor was Jan Szaster (1746-1793), a Kraków pharmacist and Doctor of Medicine.
In 1804, pharmacy training was shortened to one year in all schools of the Austrian monarchy, including the Crown School of Kraków. After the Republic of Kraków was established in 1815, a two-year pharmacy course was introduced into the Kraków School.
From 1809, the education of pharmacists took place at two faculties, namely at the Faculty of Medicine, and Philosophy. In 1809, Józef Sawiczewski was appointed Head of the Chair of Pharmacy and Medical Matter. After his death in 1825, this function was entrusted to Florian Sawiczewski, the most outstanding Pharmacy Professor of the time. In 1851, he was named Rector of Jagiellonian University.
In 1833, the Chair of Pharmacy was integrated with the Chair of General and Applied Chemistry, later a part of the Faculty of Philosophy, which substantially changed how the teaching of pharmacy was organized. In the period from 1857 to 1920, pharmacy students had their classes conducted by such renowned professors as Edward Janczewski, Józef Łazarski, Emil Czyrniański, Karol Olszewski, Zygmunt Wróblewski, Marian Smoluchowski, Rafał Czerwiakowski, Józef Rostafiński, and Władysław Szajnocha.
Amidst nationwide discussion, the teaching of pharmacy was completely reformed after Poland regained independence in 1918. Pharmaceutical departments were transformed into independent faculties of Pharmacy with four year teaching periods. The first Head of the Department of Pharmacy at Jagiellonian University was Professor Karol Dziewoński, followed by Professor Tadeusz Estreicher, who took up the post in 1926.
On the eve of World War II, the Krakow Department of Pharmacy had five separate units: Applied Pharmacy, Pharmaceutical Botany, Pharmaceutical Chemistry, Zoology for Pharmacy, and the Garden of Medical Plants, a part of the Jagiellonian University Botanical Garden.
In 1947, the Department of Pharmacy, operating within the Faculty of Philosophy, was transformed into a separate Faculty of Pharmacy. Professor Marek Gatty-Kostyal was appointed as its first dean.
The Kraków Faculty of Pharmacy entered a new era on January 1, 1950, when, along with the Faculty of Medicine, it was separated from Jagiellonian University and transformed into the Academy of Medicine.
Another milestone in the history of the Kraków Faculty of Pharmacy was the formation of the Department of Medical Analytic.
This Department, with a separate 5-year teaching program, began to function during the 1977/1978 academic year.
The year in which the Faculties of Pharmacy and Medicine were rejoined with Jagiellonian University was of special importance to the Faculty of Pharmacy. Among others, it was the first time the newly-built seat of the Department of Pharmacy on ul. Medyczna (Medyczna Street) was put to use. A modern didactic base and expanding set of research equipment allowed to extend its range of international academic and didactic cooperation as well as actively participate in the activities of the European Association of Faculties of Pharmacy (EAFP), of which the Faculty is a member since 2000. One of the consequences of this change was a considerable increase in the number of elective courses offered.
International programs carried out at the Faculty also allow for a constant perfecting of the process of education. In 2006, by decision of the Minister of Science and Higher Education, the Faculty of Pharmacy was classified as a category - A institution.