Thymoma-associated autoimmune enteropathy is a rare paraneoplastic syndrome that is characterized by severe chronic diarrhea, malabsorption, and specific histological findings. Because of its rarity, it is difficult to diagnose. We describe an adult patient with protracted diarrhea and weight loss that developed recurrent sepsis and progressive colonic stenosis due to thymoma-associated autoimmune enteropathy. Ultimately, the diagnosis thymoma-associated autoimmune enteropathy was established by characteristic intestinal histology, anti-enterocytes antibodies, and thorax imaging. Radical thymectomy was performed without improvement. Therapy with azathioprine and infliximab induced clinical remission with complete recovery of the colonic stenosis.