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Magnetic resonance cholangiopancreatography (MRCP) has not been assessed as a surrogate biomarker in pediatrics. We aimed to determine the inter‐rater reliability, prognostic utility, and construct validity of the modified Majoie endoscopic retrograde cholangiopancreatography classification applied to MRCP in a pediatric primary sclerosing cholangitis (PSC) cohort. This single‐center, retrospective, cohort study included children with PSC undergoing diagnostic MRCP between 2008 and 2016. Six variations of the Majoie classification were examined: 1) intrahepatic duct (IHD) score, 2) extrahepatic duct (EHD) score (representing the worst intrahepatic and extrahepatic regions, respectively), 3) sum IHD‐EHD score, 4) average IHD score, 5) average EHD score, and 6) sum average IHD‐EHD score. Inter‐rater reliability was assessed using weighted kappas and intraclass correlation coefficients (ICCs). Ability to predict time to PSC‐related complications (ascites, esophageal varices, variceal bleed, liver transplant [LT], or cholangiocarcinoma) (primary outcome) and LT (secondary outcome) was assessed with Harrell’s concordance statistic (c‐statistic) and univariate/multivariable survival analysis. Construct validity was further assessed with Spearman correlations. Forty‐five children were included (67% boys; median, 13.6 years). The inter‐rater reliability of MRCP scores was substantial to excellent (kappas/ICCs, 0.78‐0.82). The sum IHD‐EHD score had the best predictive ability for time to PSC complication and LT (c‐statistic, 0.80 and SE, 0.06; and c‐statistic, 0.97 and SE, 0.01, respectively). Higher MRCP scores were independently associated with a higher rate of PSC‐related complications, even after adjusting for the PSC Mayo risk score (hazard ratio, 1.74; 95% confidence interval, 1.14‐2.). MRCP sum scores correlated significantly with METAVIR fibrosis stage, total bilirubin, and platelets (r = 0.42, r = 0.33, r = −0.31, respectively; P