BackgroundWe herein report a case of a bronchogenic cyst arising from the esophagogastric junction treated by laparoscopic full-thickness extirpation. The full-thickness defect was closed by hand sewing a T-shaped line over the gastroendoscope as a bougie to prevent postoperative deformity or stenosis. Partial fundoplication (Toupet fundoplication) was added to prevent reflux.Case presentationA 32-year-old woman with a body mass index of 43 kg/m2 was admitted for treatment of a cyst-forming submucosal tumor (60 mm in diameter) on the anterior wall of the esophagogastric junction, which was detected during screening endoscopy before bariatric surgery. The tumor was an extraluminal growing type but exhibited severe erosion at the mucosal site. A cystic tumor such as a duplication cyst, bronchogenic cyst, or cyst-forming gastrointestinal stromal tumor was suspected, and the abovementioned surgery was carried out. The postoperative course was uneventful. The pathological findings revealed the tumor to be a benign bronchogenic cyst. Endoscopic examination 3 months postoperatively showed no deformity or stenosis, and the patient complained of no reflux symptoms.ConclusionThis procedure may be an efficient option for treatment of submucosal tumors on the esophagogastric junction to maintain function or avoid excessive surgery.