Accurate clinical staging of patients with cholangiocarcinoma (CCA) has a significant impact on treatment decisions. In this study, we aimed to compare the diagnostic value of magnetic resonance imaging (MRI) and 18-fludeoxyglucose positron emission tomography/computed tomography (F-FDG PET/CT) for staging of CCA. We performed comprehensive systematic search in Web of Science (including MEDLINE) and Excerpta Medica Database for relevant diagnostic studies in accordance with the preferred reporting items for systematic reviews and meta-analysis statement. Based on data extracted from patient-based analysis, we calculated the pooled sensitivity and specificity with the 95% confidence intervals (CIs). In addition, the publication bias was assessed by Deek funnel plot of the asymmetry test. The potential heterogeneity was explored by threshold effect analysis and subgroup analyses. Thirty-two studies with 1626 patients were included in present analysis. In T stage, the pooled sensitivity and specificity of MRI were 0.90 (95% CI 0.86-0.93), 0.84 (95% CI 0.73-0.91) respectively. The pooled sensitivity and specificity of F-FDG PET/CT were 0.91 (95% CI 0.83-0.95) and 0.85 (0.64-0.95) respectively. In N stage, the pooled sensitivity and specificity of MRI were 0.64 (95% CI 0.52-0.74) and 0.69 (95% CI 0.51-0.87) respectively. The pooled sensitivity and specificity of PET/CT were 0.52 (95% CI 0.37-0.66) and 0.92 (95% CI 0.79-0.97) respectively. In M stage, the pooled sensitivity and specificity of F-FDG PET/CT were 0.56 (95% CI, 0.42-0.69) and 0.95 (95% CI, 0.91-0.97) respectively. The Deek test revealed no significant publication bias. No threshold effect was identified. The subgroup analyses showed that pathological type (extrahepatic cholangiocarcinoma vs hilar cholangiocarcinoma/intrahepatic cholangiocarcinoma), country (Asia vs non-Asia) and type of MRI (1.5T vs. 3.0T) were potential causes for the heterogeneity of MRI studies and country (Asia vs non-Asia) was a potential source for F-FDG PET/CT studies. The analysis suggested that both modalities provide reasonable diagnostic accuracy in T stage without significant differences between them. We recommend that both modalities be considered based on local availability and practice for the diagnosis of primary CCA tumors. In N stage, the diagnosis of lymph node metastasis (N) of CCA is still limited by MRI and F-FDG PET/CT, due to unsatisfactory diagnostic accuracy of both. Nevertheless, F-FDG PET/CT can be used to confirm lymph node metastasis while a negative result may not rule out metastasis. Furthermore, F-FDG PET/CT have a low sensitivity and a high specificity for detection of distant metastasis.