A 42-year-old man presented with 6 months of unexplained left lower quadrant abdominal pain and hematochezia accompanied by weight loss despite extensive evaluations. Stool studies for pathogens were unrevealing, but an abdominal contrast-enhanced computed tomography revealed findings of chronic inferior mesenteric vein thrombosis. Colonoscopy demonstrated ulcerated strictures and gangrene confined to the sigmoid and descending colons, and biopsies confirmed changes of chronic irreversible colon ischemia. A homozygous Factor V Leiden mutation was diagnosed. The patient underwent colectomy and was treated with lifelong anticoagulation. While mesenteric venous thrombosis is a well-recognized cause of colon ischemia in hypercoagulable states, thrombosis of the inferior mesenteric vein is uncommon; when chronic it is rarely clinically apparent. Similarly, while Factor V Leiden mutation is a common hereditary thrombophilia, it uncommonly causes mesenteric venous thrombosis, and homozygotes of the mutation typically present earlier in the fourth decade and with non-mesenteric venous thromboembolism. This case is valuable and adds to the existing literature in describing a rare, clinically atypical, and late index presentation of homozygous Factor V Leiden mutation as chronic inferior mesenteric vein thrombosis yielding irreversible colon ischemia.