The paper focuses on research of the relationship between the State and the Catholic Church in an emergency such as the current pandemic health crisis, affecting human rights, including the fundamental right to religious freedom. In such a situation, constructive relations based on mutual respect of subjects, who are also aware of their place in a democratic society, are very important. We will illustrate the study of these relations and their development in the article in the conditions of the Slovak Republic. The article deals mainly with the period during the so-called first wave of the Covid-19 pandemic in Slovakia. Although other waves of the pandemic have already passed, it seems that restrictions on religious freedom have not been sufficiently analyzed.