We present a 2-month-old male infant with thrombosis in the superior vena cava and pericardium due to transient protein C deficiency. Protein C deficiency was related to sepsis and hepatitis-induced liver function impairment. The patient’s cardiac anatomy was otherwise normal. The patient was referred to us with signs of superior vena cava syndrome. Pericardial mass was excised. Pathological examination diagnosed the mass as organized thrombus. After the operation, signs of superior vena cava syndrome totally resolved. Serial echocardiographic examinations revealed regression of thrombus in the superior vena cava. This is the first case reported in the literature with intrapericardial thrombus secondary to transient protein C deficiency.