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For patients refusing surgical treatment for deep early gastric cancer, hybrid natural orifice transluminal endoscopic surgery with sentinel lymph node navigation is a potential treatment option, particularly when the anatomic location of the cancer has low probability of lymph node metastasis. We report a case of deep early gastric cancer of the fundus beyond the endoscopic submucosal dissection indication that was treated by hybrid natural orifice transluminal endoscopic surgery with sentinel lymph node navigation. In a conventional approach, a total gastrectomy would have been needed; however, the patient refused surgical intervention. In this case, since the patient showed no positivity of the sentinel lymph node on intraoperative navigation, laparoscopic basin lymph node dissection was not performed. Hybrid natural orifice transluminal endoscopic surgery might be considered for specific regions such as the safety zone where lymph node metastases are less likely to occur.