We report a case of a 33-year-old female patient with Budd-Chiari syndrome because of polycythemia vera. A transjugular intrahepatic portal-systemic shunt was performed because of refractory ascites 7 months after diagnosis. She had a stable hepatic function receiving anticoagulants until 3 years later when she presented with bloody diarrheas, liver function deterioration with prolonged prothrombin time and hypoalbuminemia, encephalopathy, and ascites. Colonoscopy revealed ulcerative pancolitis and the patient was treated with corticosteroids and antibiotics. Hepatic function was stabilized in parallel to controlling ulcerative colitis and the patient is in good health until now receiving maintenance therapy for ulcerative colitis and anticoagulants for Budd-Chiari syndrome.