Despite endoscopic resection has been performed to treat gastric gastrointestinal stromal tumor (GISTs). However, the safety and long-term outcomes remains controversial. This study aims to compare the safety and surgical outcomes of endoscopic versus laparoscopic resection of gastric GISTs. A total of 335 patients that were pathologically confirmed with gastric GISTs (tumor size ≤ 3.5 cm) were surgically treated with endoscopic resection (endoscopic group) or laparoscopic resection (laparoscopic group) in three institutions from March 1, 2011 to October 1 2014. These demographics, tumor characteristics, and outcomes were retrospectively analyzed for identification of outcomes and feasibility of endoscopic or laparoscopic resection. Of 335 patients, 262 and 73 patients underwent endoscopic and laparoscopic resection, respectively. The average tumor size was 1.33±0.78 cm in the endoscopic group and 1.97±0.93 cm in the laparoscopic group. The average operating time was 62.40±36.94 min in the endoscopic group and 112.81±55.69 cm in the laparoscopic group. Days of realimentation was 2.76±1.67 in the endoscopic group and 4.89±2.03 in the laparoscopic group. The average cost was $ 3246.01±1017.61 in the endoscopic group and $ 4884.81±1339.51 in the laparoscopic group. There was no postoperative mortality. Endoscopic resection for gastric GISTs is safe and feasible in tumors ≤ 3.5 cm. Because endoscopic resection showed good results with lower operating time, realimentation days, length of hospital stay and mean total cost, it is a minimally invasive and safe alternative approach which can achieve fast recovery and satisfactory outcomes for appropriately selected patients with gastric GISTs.