It is known that with a new coronavirus infection (SARS-CoV-2), even despite the use of anticoagulant therapy, there is a high frequency of both venous and arterial thrombosis, often leading to the death of the patient. Our publication presents a case of treatment of right-sided post-pneumonic pleural empyema (as a result of a new coronavirus infection and right-sided polysegmental destructive pneumonia) complicated by pulmonary embolism. Despite the successful treatment of the underlying disease, the fatal outcome came quickly and suddenly. This case shows that the risk of thrombosis in patients after COVID-19 can persist for a long time even when the presence of the virus in the body is no longer determined. Additional studies of the pathophysiological mechanisms and clinical features of these patients are needed to select the optimal therapeutic strategy.