The beginnings of the study of modern pharmacy in the Slovak Republic can be traced back to the war division of Czechoslovakia. An important milestone was the start of a two-year study programme during the academic year 1939–1940 in the form of an interfaculty collaboration: part of the programme was covered by the Faculty of Arts and the other part by the Faculty of Medicine. In 1940 government regulations prolonged the length of study to three years, with a secondary-school leaving certificate and one year of professional experience in pharmacy as a prior condition to entering the University. In 1945, after the restoration of Czechoslovakia, the need arose to unify the pharmaceutical education within the Republic. In 1948 the law on pharmaceutical study took force and unified the pharmaceutical study in Czechoslovakia. The length of study was extended to four years.
The independent Faculty of Pharmacy of Comenius University (Slovak University at that time) was established by the government regulation which came into effect on September 1, 1952. The first dean of the University was Ľ. Krasnec and vice-dean L. Zathurecký. Since the academic year 1953–1954 the pharmaceutical programme was extended to five years. The work on construction of a new building for the Faculty of Pharmacy on Odbojárov Street begun in 1958. It was opened in 1960. During the same year the two pharmaceutical faculties in Brno and Bratislava merged and Bratislava became the residence of the only national Faculty of Pharmacy in Czechoslovakia. This was one of the most significant periods of the Faculty. Later the Faculty of Pharmacy of Charles University with its headquarters in Hradec Králové was established.
In the area of educational activities, approval of study programme change to a differentiated three-field study in 1977 meant the creation of the following study fields: general pharmacy, technological pharmacy and clinical pharmacy. This form of study continued until 1990 when an independent five-year long study of pharmacy was introduced.
Currently the Faculty provides Master Study Programme ‘Pharmacy’ which is fully compatible with the system of preparation of pharmacists within the EU. Since 2002 the Faculty also provides the study for Bachelor degree in Sanitary and Diagnostic Devices. Apart from the educational work an important part of the Faculty life consists of scientific and research activities which have been oriented mainly on separate aspects of drugs and medicines. Before 1989 research work used to be coordinated within the frame of the state plan of research, these days it is supported mainly by national and international grant agencies.