Since its appearance at the end of 2019, the disease of the COVID-19 virus has grown from the local level into a global pandemic that has not bypassed the Republic of Serbia. The COVID-19 pandemic has affected the health system, the economy and the general condition of the population. Depending on the available hospital and staff capacities, each of the countries affected by the COVID-19 pandemic has established measures to struggle and treat citizens affected by the pandemic. In the newly created conditions, state-owned health care institutions and the Republic of Serbia focused their capacities on treatment and rehabilitation of COVID-19 patients, which had an impact on the management, organization of work and efficiency of health care institutions as well as additional costs for the overall health care system in the period from March 2020 to January 2022. This study shows the effects of the pandemic on the performance and costs of state-owned health facilities with a special focus on acute inpatient facilities in the Republic of Serbia. Medical analysis consists of: differences in the total number of patients, outpatients, changes in the number of visits in the private sector, the value of the case-mix index, the number of operations in acute hospitals, day hospital procedures, and consumption of reserve antibiotics. The financial analysis consists of: allocations for health in the budget of the Republic of Serbia, investments in public health, additional allocations due to the COVID-19 pandemic, analysis of the budget of the Health Insurance Fund (HIF), expenditures on salaries, drugs and medical supplies, cost per day, and average cost per patient. The result of the COVID-19 pandemic is a decline in elective operations and the number of outpatient visits and, on the other hand, an increase in spending in the health sector, as a result of significant growth in investment in tertiary institutions and in new hospitals, wages and overall current spending.