A 36-year-old Japanese man known to have incomplete Behçet’s disease (oral aphthous ulcers, genital ulcers, skin lesions, and esophageal and ileocecal ulcers) was admitted to our hospital in January 2011 for abdominal pain. We administered corticosteroids and immunosuppressants. Two months later, we performed an ileocecal resection to control gastrointestinal bleeding from the ileocecal ulcers. High fever persisted after this surgery, and upper gastrointestinal endoscopy demonstrated ulcer penetration between the lower and abdominal esophagus. Eighteen days after the initial ileocecal resection, we performed a lower esophagus resection, gastric tube reconstruction and enterostomy, during which we confirmed a 5-mm-dia. perforated site at the posterior wall of the abdominal esophagus. Postoperative anastomotic leakage and empyema occurred, but they were relieved by thoracic drainage and empyema dissection.