Noninvasive monitoring of disease activity in autoimmune hepatitis (AIH) has potential advantages for patients for whom liver biopsy is invasive and with risk. We sought to understand the association of multiparametric magnetic resonance imaging (mpMRI) with clinical course of patients with AIH. We prospectively recruited 62 patients (median age, 55 years; 82% women) with clinically confirmed AIH. At recruitment, patients underwent mpMRI with LiverMultiScan alongside clinical investigations, which were repeated after 12‐18 months. Associations between iron‐corrected T1 (cT1) and other markers of disease were investigated at baseline and at follow‐up. Discriminative performance of cT1, liver stiffness, and enhanced liver fibrosis (ELF) to identify those who failed to maintain remission over follow‐up was investigated using the areas under the receiver operating characteristic curves (AUCs). Baseline cT1 correlated with alanine aminotransferase (Spearman’s correlation coefficient [rS] = 0.28, P = 0.028), aspartate aminotransferase (rS = 0.26, P = 0.038), international normalized ratio (rS = 0.35 P = 0.005), Model for End‐Stage Liver Disease (rS = 0.32, P = 0.020), ELF (rS = 0.29, P = 0.022), and liver stiffness rS = 0.51, P < 0.001). After excluding those not in remission at baseline (n = 12), 32% of the remainder failed to maintain remission during follow‐up. Failure to maintain remission was associated with significant increases in cT1 over follow‐up (AUC, 0.71; 95% confidence interval [CI], 0.52‐0.90; P = 0.035) but not with changes in liver stiffness (AUC, 0.68; 95% CI, 0.49‐0.87; P = 0.067) or ELF (AUC, 0.57; 95% CI, 0.37‐0.78; P = 0.502). cT1 measured at baseline was a significant predictor of future loss of biochemical remission (AUC, 0.68; 95% CI, 0.53‐0.83; P = 0.042); neither liver stiffness (AUC, 0.53; 95% CI, 0.34‐0.71; P = 0.749) nor ELF (AUC, 0.52; 95% CI, 0.33‐0.70; P = 0.843) were significant predictors of loss of biochemical remission. Conclusion: Noninvasive mpMRI has potential to contribute to risk stratification in patients with AIH.