Although the prison population has always been exposed to certain health and other crisis situations to a greater or lesser extent, the COVID-19 pandemic has shown, like never before, how much the protection of human rights (to life and health) of persons deprived of liberty is a challenging task for judicial bodies and civil society organizations. Even in "old normal" times, people in penal institutions are an extremely vulnerable group because prisons are places prone to the spread of infectious diseases due to the higher prevalence of risk factors for infection such as unavoidable close contact, overcrowding, poor ventilation, limited access to health services. The risk group are not only prisoners, but also visitors, as well as employees who often work in overcrowded conditions and suffer from insufficient resources. In the COVID-19 pandemic, prison systems around the world have been under great pressure to limit the impact of the disease and to keep it outside prison walls for as long as possible to ensure living and working conditions for inmates and staff. In addition to general epidemiological guidelines and measures, each country made specific regulations how to deal with the pandemic within the prison system. The purpose of this thesis was to investigate functioning of prison systems with regard to ensuring the protection of the human rights of prisoners and employees and the execution of prison sentences on a global and national level in the public health crisis caused by the coronavirus (2020-2022). Thesis used a combined research methodology on a descriptive level. According to the combined empirical research design, quantitative methodology (structured interview) is used for the collection of primary data on the functioning of the Penitentiary in Lepoglava. A qualitative methodology is used for processing the primary data obtained in this way. To identify problem categories, a qualitative analysis of the transcription of the structured interview was conducted. Archive (desk) methods (analysis of literature and documents, statistical analysis) and methods of induction and deduction were used to collect and process secondary data for the purpose of synthesizing the problem and theoretical framework and statistical data. Statistical analysis performed at the sample level provided answers to all previously stated research questions. The obtained results indicate that the COVID-19 pandemic has fully affected the functioning and organization of prison systems, as well as the social, physical and mental health of prisoners and employees, and that prison systems, when achieving the tasks of executing prison sentences, introduced measures and made adjustments in to the organization of work with the aim of prevention and control over the outbreak of the disease COVID-19 so that all persons in penal institutions remain healthy and safe, while enabling the realization of the basic human rights of prisoners and their employees. Although, due to the implementation of epidemiological measures, there was a certain limitation of the realization of the fundamental rights of prisoners, that is, the realization of group treatment activities, at the national level, an increase in the number of individual treatment of prisoners, educational programs and programs of work activities was recorded at the same time. Based on deeper insights and obtained results, the operation of the Lepoglava Penitentiary in the public health crisis caused by the COVID-19 pandemic can be considered an example of good practice in the context of rehabilitation and resocialization of prisoners and the preservation of the fundamental rights of prisoners and employees. In this sense, the professional contribution of this thesis can be considered.