We describe a case of altered bowel habit, early satiety, anorexia and weight loss caused by autoimmune enteropathy. This diagnosis was confirmed by biopsies obtained from upper gastrointestinal endoscopy and ileocolonoscopy. Further investigations revealed multiple pulmonary nodules which were metastases from a malignant thymoma. The patient was commenced on oral budesonide and Mesalazine, in addition to oral and enteral supplementation driven by the specialist nutrition support team, but she did not achieve histological remission, nor did she demonstrate improvement in her nutritional status. She received 3-weeks of in-patient parenteral nutrition, but then subsequently deteriorated as she declined home parenteral nutrition. The patient died eight months later from complications of her disease. This case highlights the rare manifestation of metastatic thymoma presenting with autoimmune enteropathy that led to intestinal failure and death.