Magnetic resonance cholangiopancreatography (MRCP), MRCP after secretin stimulation (S-MRCP) and endoscopic ultrasonography (EUS) are all selected to diagnose pancreas divisum. However, the accuracies of three diagnosis remain unclear. The aim is to address the diagnostic accuracies of MRCP, S-MRCP and EUS on pancreas divisum. We searched PubMed, MEDLINE and EMBASE databases from inception to January, 2015. Of the 536 citations retrieved, 16 studies were included. For MRCP diagnosis on pancreas divisum, the area under the hierarchical summary receiver-operating characteristic (HSROC) curve was 0.90 (95% confidence interval [CI] 0.87 to 0.92), and for S-MRCP and EUS, 0.99 (95% CI 0.97 to 0.99) and 0.97 (95% CI 0.96 to 0.98). Sensitivity and specificity for MRCP were 0.59 (95% CI 0.45 to 0.71) and 0.99 (95% CI 0.96 to 1.00); for S-MRCP, 0.83 (95% CI 0.66 to 0.92) and 0.99 (95% CI 0.96 to 1.00); for EUS, 0.85 (95% CI 0.67 to 0.94) and 0.97 (95% CI 0.90 to 0.99). Comprehensive comparison of three diagnostic techniques to pancreas divisum, S-MRCP was more reliable than MRCP and EUS on the effect of the diagnostic test.