The Faculty of Health Protection, today known as the Faculty of Health Sciences, was established through the transformation of the Faculty of Nursing, which continued the tradition of educating nurses at the master’s level initiated in 1975 (nursing education in Kraków itself began earlier, in 1911, within the framework of the School of Nursing). In 2005, the Faculty of Health Sciences held its first admissions for undergraduate midwifery studies. In the same year, the name of the Institute of Nursing was changed to the Institute of Nursing and Midwifery. The Faculty also refers to the more than century-old idea—and today, the interdisciplinary field—of public health, continuing the activities of the School of Public Health, established in 1991 as an interfaculty unit of the Medical Academy and the Jagiellonian University. In 1997, the School became the Institute of Public Health. The Department of Emergency Medical Services provides education in this field. Initially, training of paramedics was conducted as a specialization within the Nursing program (the first intake took place in 2001). From 2004, this specialization was carried out within the Public Health program, while in 2007 the first recruitment was launched for Emergency Medical Services as an independent degree program. On January 15, 2009, the Department of Emergency Medical Services was separated from the structure of the Institute of Public Health and transformed into an independent unit of the Faculty. Since 1998, the Faculty of Health Sciences has also offered studies in physiotherapy. In 2001, an agreement was signed in Kraków between the Małopolska Region and the Jagiellonian University to jointly reform the training system for the profession of physiotherapy technicians.

As a result, admissions to the physiotherapy program at the Faculty were increased, the Medical Vocational School No. 4 in Kraków was closed, and the Faculty fully took over the training. The Institute of Physiotherapy, comprising units serving as the teaching and research base for this program, was established in 2006. In response to the dynamic development of medical imaging in Poland and worldwide, there arose a need for a greater number of qualified specialists to operate modern diagnostic equipment. To meet this demand, the Faculty of Health Sciences, within the Institute of Physiotherapy, launched a degree program in electroradiology, offering graduates an opportunity to obtain a promising and forward-looking profession and to secure attractive employment opportunities. The establishment of the Faculty was a response to the new socio-economic situation in Poland resulting from healthcare reform and the changing labor market. These transformations required setting new priorities in education. A fresh approach to the training of healthcare professionals was shaped by several factors: a new philosophy of healthcare management, the shift from medical care to health promotion and disease prevention, strong emphasis on primary healthcare, and the significant development of medical technologies. It was necessary to meet the demand for highly qualified healthcare professionals to fill senior and middle management positions, as well as to ensure a supply of specialized medical personnel (nurses, physiotherapists, midwives, paramedics, and sanitary inspectors).