The History of the Public Health Institute begins with the founding in Kraków of an interdepartmental unit of the Medical Academy - the School of Public Health in 1990. As the first school of its kind in Poland, it was started with advisory assistance from France's Ministry of Health and was modelled on the French Ecole Nationale de Sante Publique. The School was headed by Tadeusz Skarbek PhD, who was then succeeded by Andrzej Ryś MD.
In 1991, the School staff launched an intensive and multidirectional educational initiative geared towards the preparation of modern managerial personnel for Poland's health care system. To this end, the School offered two-year postgraduate courses in hospital management and public administration, and 1993 saw the launch of three-year postgraduate studies for acting health care managers. The curricula were based on the programmes of the Harvard School of Public Health in the area of policy and management in health care.
In 1997 Postgraduate Courses in Health Promotion began for health care professionals engaged in developing and implementing health care programmes. The curriculum was developed within a project funded by the European Commission's Tempus programme and is based on similar educational ventures operating in Holland. In 1992 the School of Public Health joined the Association of Schools of Public Health in European Region (ASPHER), and in 1995 its curricula earned the Association's accreditation.
In February 1997, by a resolution of Jagiellonian University Senate, the School of Public Health became part of the University's Collegium Medicum, changing its name to Public Health Institute to form, in conjunction with the Institute of Nursing, the Health Care Department (at present, the Department also contains the Institute of Rehabilitation). Professor W. Cezary W³odarczyk was appointed Director of the Institute. Also in 1997 the Institute opened five-year B.A. and M.A. courses that cater for the future administrative and management staff of the public health care system. In 2002 the Institute saw its first M.A. graduates emerge.
From September 2002 to September 2008, the Institute's Director was Professor Stanisława Golinowska. From September 2008 the Institute's Director was Professor Andrzej Pająk. From September 2012 until September 2016 the Institute's Director was Prof Cezary W. Włodarczyk. Since September 2016 the Institute's new Director has been dr hab Christoph Sowada.