Dual-layer spectral detector computed tomography (DLCT) can detect noncalcified biliary stones. The diagnostic ability of DLCT for detecting biliary stones may be comparable to that of magnetic resonance cholangiopancreatography (MRCP). This study seeks to compare the diagnostic ability for biliary stones between these two imaging modalities. This retrospective study included 102 cases with a diagnosis of biliary stones including gallstones (n = 66) and common bile duct (CBD) stones (n = 25) or spontaneously passing CBD stones (n = 11). The reference standard used was operative findings, endoscopic retrograde cholangiopancreatography or follow-up over 6 months. In DLCT, 120-kVp images, 40-keV virtual monoenergetic images and material decomposition images were created. We compared the diagnostic ability of DLCT and MRCP for biliary stones using the McNemar's test. The sensitivity and specificity of DLCT versus MRCP for biliary stones were 91.2% versus 95.6% and 90.9% versus 90.9%. Thus, the sensitivity and specificity were not significantly different (P = 0.25 and P = 1.0). Although in small stones (<9 mm) the sensitivity of calcified stones was not different between DLCT and MRCP (100% versus 92.5%), the sensitivity of noncalcified stones in DLCT was lower than that in MRCP (38.5% versus 100%). The diagnostic ability of biliary stones in DLCT appears comparable to that of MRCP in overall cases. However, detecting noncalcified stones less than 9 mm in size is limited in DLCT.