A rare case of inferior vena cava (IVC) thrombosis and pulmonary embolism secondary to acute exacerbation of chronic pancreatitis was reported. Radionuclide venography and lung perfusion scintigraphy were performed on a 46-year-old male with acute exacerbation of chronic pancreatitis who complained of mild swelling of a leg and shortness of breath. Scintigraphy showed an abnormal large hot spot at the level of the pancreas and a pulmonary embolism. Enhanced abdominal CT revealed an IVC thrombus and a cystic mass adjacent to the IVC. Despite the absence of severe abdominal pain, the serum amylase and elastase-1 levels were very high. These findings indicated that a pancreatic cyst had penetrated into the IVC, where it triggered the formation of a thrombus and caused a pulmonary embolism. Scintigraphic examination was useful for the evaluation of this rare condition.