Objective: To compare the safety and efficacy between laparoscopic and open surgery in treatment of choledochal cyst by using Meta-analysis. Methods: The retrospective or case-control studies comparing laparoscopic versus open surgery for choledochal cyst in children were searched from the national and international databases. Meta-analysis was performed after literature screening according to the inclusion criteria. Results: Ten studies were finally included, involving a total of 1 394 patients, of whom, 589 cases underwent laparoscopic surgery (laparoscopic group) and 805 cases underwent open surgery (open surgery group). In laparoscopic group compared with open surgery group, the operative time was prolonged (WMD=54.51, 95% CI=24.37–84.64, P<0.05), while the intraoperative blood loss was reduced (WMD=–16.27, 95% CI= –21.16––11.39, P<0.05), time to first postoperative flatus and food intake was shortened (WMD=–1.2, 95% CI= –1.22––1.18; WMD=–1.31, 95% CI=–1.62––1.00, both P<0.05), and length of postoperative hospital stay and incidence of postoperative complications were decreased (WMD=–3.04, 95% CI=–4.08––2.36; OR=0.37, 95% CI=0.15–0.90, both P<0.05). Conclusion: Laparoscopic surgery has shown superiority in treatment of choledochal cyst compared with open surgery. With the improvement of laparoscopic techniques and deftness of surgeon’s practice, laparoscopic surgery may become the first choice procedure for choledochal cyst.