A laparoscopic wedge resection for a submucosal tumor, which is close to the gastroesophageal junction, is technically challenging. This can be a dilemma to both patients and surgeons when the tumor margin involves the gastroesophageal junction because a wedge resection in this situation might result in a deformity of the gastroesophageal junction or an injury to the lower esophageal sphincter, which ultimately results in lifelong gastroesophageal reflux disease. The patient was a 42 year-old male, whose preoperative endoscopic ultrasonographic finding did not rule out a gastrointestinal stromal tumor. He underwent a laparoscopic gastric wedge resection and prophylactic anterior partial fundoplication (Dor) and was discharged from hospital on the fifth postoperative day without any complications. There were no symptoms of reflux 5 months after surgery. A laparoscopic wedge resection and prophylactic anti-reflux surgery might be a good surgical option for a submucosal tumor at the gastroesophageal junction.