Background: Endoscopic submucosal dissection (ESD) is widely used as an effective treatment of early gastric and esophageal tumors, as it is minimally invasive, safe, and convenient. Epigastric pain is a common complication of ESD. In the traditional cognition, the postoperative pain of ESD is not serious and does not attach too much attention. However, previous studies found that the incidence of moderate to severe pain after ESD can be as high as 44.962.8%. At present, there is no unified understanding of how to carry out good postoperative analgesia in patients undergoing ESD of stomach and esophagus. The purpose of present study is to investigate the efficacy of intraoperative dexmedetomidine (DEX) using on postoperative pain though observing the postoperative visual analog scale (VAS) score within 48 h after ESD surgery, so as to explore an effective analgesia and anesthetic method in patients undergoing gastric and esophagus ESD. Methods/design: This study is a prospective, single-center, two-arm, randomized control trail. In total, 120 patients undergoing endoscopic submucosal dissection were stratified by type of surgery (i.e., gastric or esophagus ESD) and randomized into two treatment groups, DEX group (group D, n = 60) and control group (group C, n = 60). Patients in the experimental group (DEX group) will be administrated a loading dose of DEX at 1 mu g/kg for 15 min and a continuous infusion at 0.6 mu g/kg/h until 30 min before the end of operation. In control group, the same volume of normal saline was infused. The primary outcome is VAS at 2 h after ESD surgery. The secondary outcome will be VAS at 1 h, 4 h, 6 h,1 8 h, 24 h, and 48 h, the status of perioperative hemodynamics, the use of remedial analgesics, sedation score, shivering, postoperative nausea and vomiting (PONV), and satisfaction scores of patient and complication of ESD (such as bleeding, perforation, aspiration pneumonia). Discussion: The results of this study will demonstrate that intraoperative application of DEX is beneficial for postoperative pain treatment in patients undergoing ESD. This study will not only confirm that postoperative pain treatment is necessary for patients undergoing ESD but also provides an effective anesthesia method for postoperative analgesia.