Mesenteric vein thrombosis (MVT) is a rare but lethal disease. We recently treated a patient with MVT probably caused by polycythemia vera (PCV). A 68-year-old woman with a prior medical history of PCV was admitted to our surgical unit for vague abdominal pain and vomiting. A CT scan of the abdomen showed MVT. Because there was no evidence of intestinal ischemia, the patient was treated with anticoagulation therapy. However, when a physical examination seven days later revealed signs of peritoneal irritation, surgery was performed immediately. Laparotomy demonstrated a large segment of necrotic small bowel, and resection of the long, infarcted intestine with primary end-to-end anastomosis was performed. Anticoagulation therapy was administered after the procedure, the patient progressed well, and there have been no signs of recurrence as of 12 months after the operation. This case demonstrates that early recognition of MVT in the clinical course of PCV, and appropriate treatment can improve the outcome.