Objective To evaluate the feasibility and safety of endoscopic treatment for gastric stromal tumors with maximum diameter of 3 to 5 cm. Methods From April 2010 to April 2016， a retrospective analysis was performed on the data of patients with gastric stromal tumors undergoing endoscopic （29 cases） or laparoscopic （26 cases） resection in the First Affiliated Hospital of Soochow University. Baseline data， perioperative data and follow-up data were collected and analyzed. Results There was significant difference on tumor location between the two groups （χ2=12.173， P=0.007）. Tumors mainly located at gastric fundus in the endoscopic group （65.5％， 19／29）， while at gastric body in the laparoscopic group （61.5％， 16／26）. Compared with the laparoscopic group， patients in the endoscopic group had shorter operation time ［45 （35， 60） min VS 70 （60， 85） min， U=686.000， P＜0.05］， lesser intraoperative blood loss ［15 （10， 15） mL VS 20 （10， 20） mL， U=513.000， P=0.017］， and earlier recovery time of gastrointestinal function ［12 （6， 24） h VS 20 （18， 24） h， U=585.500， P＜0.001］. Compared with the laparoscopic group， the patients in the endoscopic group had a higher complication rate ［55.2％ （16／29） VS 11.5％ （3／26）， χ2=11.543， P＜0.001］ and a lower intact tumor removal rate ［89.7％ （26／29） VS 100.0％ （26／26）， χ2=23.989， P＜0.001］. The other perioperative parameters such as the incidence of intraoperative major bleeding, postoperative peritonitis， postoperative fasting time， hospitalization time and total hospitalization expenses showed no statistical different （all P＞0.05）. The postoperative follow-up time was 30.0 （17.5， 50.0） and 38.5 （26.0， 49.8） months in the endoscopic and laparoscopic group， respectively. There was no significant difference in the recurrence rate between the two group ［3.4％ （1／29） VS 7.7％ （2／26）， χ2=0.009， P=0.922］. Conclusion Endoscopic resection may be an alternative therapeutic approach for large gastric stromal tumors with shorter operation time， less intraoperative blood loss， and earlier recovery time of gastrointestinal function.