Studies have reported that cholecystectomy may increase the risk of cholangiocarcinoma. However, this association is controversial. Thus, we conducted a systematic review and meta-analysis to explore the relationship between cholecystectomy and the risk of cholangiocarcinoma. Relevant studies were identified by searching PubMed, EMBASE, ISI Web of Science published before February 2017. We used the random effects model proposed by DerSimonian and Laird to quantify the relationship between cholecystectomy and risk of cholangiocarcinoma. Publication bias was evaluated using funnel plots, Begg's and Egger's tests. Subgroup and sensitivity analyses were performed to validate the stability of the results. 16 articles, comprising 220,376 patients with cholecystectomy and 562,392 healthy controls, were included in our research. Our meta-analysis suggested that the risk of cholangiocarcinoma was significantly higher in the cholecystectomized patients in comparison with healthy controls, with heterogeneity among studies (summary odds ratio [OR] = 0.72; confidence interval [CI] = 0.55-0.90; I = 69.5%). Additionally, this association was also observed in cohort studies (OR = 0.83; 95% CI = 0.73-0.94) and case-control studies (OR = 0.60; 95% CI = 0.40-0.80). However, When the intrahepatic cholangiocarcinoma and extrahepatic cholangiocarcinoma were analyzed separately, the present study only indicated cholecystectomy was associated with increased the risk of extrahepatic cholangiocarcinoma (OR = 1.19; 95% CI = 0.32-2.05), rather than intrahepatic cholangiocarcinoma (OR = 1.19; 95% CI = 0.32-2.05). In conclusion, cholecystectomy was associated with a significant 54% increase in the risk of cholangiocarcinoma, especially in the extrahepatic cholangiocarcinoma.