To compare the safety and efficacy between laparoscopic and open cyst excision with hepaticojejunostomy for children with choledochal cysts using meta-analysis. Studies comparing the laparoscopic and the open choledochal cyst excision that met the inclusion criteria for data extraction were identified from electronic databases (PubMed, Embase, Science Citation Index, and the Cochrane Library) up to November 2014. The proceedings of relevant congress were also searched. The outcomes were operative time, intraoperative blood loss, time to food intake, postoperative morbidity and mortality, length of hospital stay. Outcomes were calculated as odds ratios (ORs) with 95 % confidence intervals (CIs) using RevMan 5.2. Seven retrospective studies were finally included, involving a total of 1016 patients, of whom, 408 cases underwent laparoscopic cyst excision and Roux-en-Y hepaticojejunostomy (LH) and 608 cases underwent open cyst excision and Roux-en-Y hepaticojejunostomy (OH). In LH group compared with OH group, the operative time was longer (MD = 59.11, 95 % CI 27.61-90.61, P = 0.0002), while the length of postoperative hospital stay was less (MD = -2.01, 95 % CI -2.49 to -1.54, P < 0.00001), the intraoperative blood loss was lower (MD = -37.14, 95 % CI -66.69 to -7.60, P = 0.01) and time to food intake was less (MD = -1.14, 95 % CI -1.61 to -0.67, P = 0.01). The rate of postoperative morbidity was more in the OH group, but there is no statistically significant difference between the two groups in postoperative morbidity (OR = 0.52, 95 % CI 0.13-2.06, P = 0.35). Laparoscopic surgery is a feasible, safe treatment of choledochal cyst with less postoperative morbidity, a shorter length of stay and a lower blood loss when compared with open approach. With the improvement of laparoscopic techniques and deftness of surgeons practice, laparoscopic surgery may become the first choice procedure for choledochal cyst.