Incidences of obesity, obesity surgeries, and gastric submucosal tumors (GST) have increased worldwide. This case report aims to demonstrate that concomitant laparoscopic transgastric resection (LTGR) of a gastrointestinal stromal tumor (GIST) near the esophagogastric junction (EGJ) can be performed safely and effectively in a patient with morbid obesity and scheduled sleeve gastrectomy (SG).The patient was planned to undergo SG surgery after the diagnosis of morbid obesity (BMI, 40.4 kg/m). The routine preoperative endoscopic examination revealed a 4-cm diameter GIST-compatible lesion in the stomach near the EGJ. The LTGR with concomitant SG was scheduled for the patient.The ports were placed for laparoscopic SG. Greater curvature and gastric fundus were fully mobilized. Along the greater curvature gastrotomy was performed, and thus the tumor was localized. The tumor was resected with a linear stapler by considering surgical margins. The frozen section examination showed no malignancy. The gastrotomy was closed, and the SG was performed via the orogastric tube (39F). In the postoperative passage X-ray, there was no stenosis or leaking, and the patient was externed on the third postoperative day. In the immunohistochemical examination, it was reported that the tumor was a GIST, and the surgical margins were negative.The LTGR may help to protect the stomach or minimize the degree of partial resection in the treatment of especially GSTs near the EGJ.