The paper analyzes the impact of the COVID-19 pandemic on the rights of prisoners and the prison system. It begins by presenting preventive measures implemented in the Republic of Croatia, as well as internationally, to prevent the further spread of COVID-19 within the prison system. After that, the impact of extraordinary measures on the rights of prisoners in Croatia is analyzed through the reports of the Ombudsman for 2020 and 2021 and selected decisions of the Constitutional Court of the Republic of Croatia. Since many of the prisoners' conventional rights were restricted or derogated during the pandemic, and states interpreted their obligations under the Convention differently, a separate chapter is dedicated to the European Convention on Human Rights in the context of the pandemic. Special attention is also given to the issue of pre-trial detention during the pandemic, particularly due to the extraordinary measure of holding remote hearings, as this procedure often led to less favorable decisions for the defendant. Before the conclusion, a brief overview of the legislative framework and the system of supervision over extraordinary measures is provided. In addition, it is also considered whether the prisoners were sufficiently informed about the measures that were adopted due to the pandemic, which often had a negative impact on the exercise of their rights. The conclusion evaluates the state's response to this pandemic and its effects on prisoners and the prison system, highlighting what, in the author's opinion, was done well and what needs improvement in future health crises.