Vaginal natural orifice transluminal endoscopic surgery (vNOTES) is an innovative minimally invasive procedure. The study aimed to evaluate whether vNOTES achieves non-inferior results compared to conventional laparoscopy in patients undergoing ovarian cystectomy. Participants with benign ovarian tumors were randomly assigned (1:1) to undergo laparoscopy or vNOTES. Randomization was stratified based on the size of the ovarian tumor. Patients and surgeons were aware of the allocated procedures. The primary outcome was the proportion of patients successfully treated by the allocated procedure (non-inferiority hypothesis, margin of 15%). The secondary outcomes included operative time, estimated blood loss, time for specimen retrieval, postoperative pain score, use of analgesics, time to first flatus, and perioperative complications. Sixty-four patients were randomly assigned to laparoscopy (n = 32) and vNOTES (n = 32) and were included in the intention-to-treat analysis. The success rates were 100% and 96.9%, respectively. Non-inferiority of vNOTES was demonstrated, as the lower limit of the one-sided 95% confidence interval for the stratified risk difference was -12.7%, which lies above the pre-specified non-inferiority margin of -15%. The vNOTES group exhibited lower pain scores, with a median difference of -1 (95% CI -1 - -1, p < 0.001). vNOTES demonstrates non-inferiority to laparoscopy for ovarian cystectomy in selected patients, with notable advantages in cosmetic outcomes and reduced postoperative pain. ChiCTR2300070890.