Laparoscopic gastrectomy is commonly performed for gastrointestinal stromal tumors (GISTs). Partial gastrectomy is usually achieved with a wedge resection to preserve gastric function; however, performing a wedge resection to excise a large tumor located close to the esophagogastric junction (EGJ) can result in deformation of the stomach and/or the stenosis of the EGJ if the gastric wall resection is excessive. We describe our procedure, in which the whole layer of the gastric wall was cut, maintaining a sufficient margin and confirming the distance between the tumor and the EGJ, by endoscopy and laparoscopy. The defect in the gastric wall was closed using linear staplers by hanging up the stay sutures. Five patients with GIST close to EGJ underwent this procedure, followed by a good postoperative course. Thus, we consider our procedure to be safe and effective for gastric GISTs close to the EGJ.