To investigate the added value of using contrast-enhanced magnetic resonance imaging (MRI) in conjunction with contrast-enhanced computed tomography (CT) for differentiating malignant and benign ampullary strictures. The present retrospective study included 90 patients with ampullary strictures who underwent preoperative contrast-enhanced CT and contrast-enhanced MRI at two tertiary institutions. The image sets (i.e., CT alone vs. combined CT and MRI) were evaluated by three abdominal radiologists, who used a five-point Likert scale to score their confidence for diagnosing malignancy in patients with ampullary strictures. Diagnostic accuracy was calculated using receiver-operating characteristic (ROC) curve analysis, sensitivity, specificity, and accuracy. Additionally, interobserver agreement regarding the scoring of potential malignancies of the ampullary strictures was assessed. The addition of contrast-enhanced MRI to contrast-enhanced CT showed a significant improvement in predicting malignant ampullary strictures in all three observers (p = 0.007, 0.001, and 0.002) using ROC curve analysis, and a significant improvement was observed in diagnostic sensitivity and accuracy for predicting malignancy (p = 0.016 and 0.029 for observer 1; p = 0.023 and 0.010 for observer 2; and p = 0.010 and 0.011 for observer 3). The interobserver agreement for the five-point scale in determining malignancies of the ampullary strictures was 0.86 for CT alone and 0.93 for the combined set of CT and MRI. The addition of contrast-enhanced MRI to CT provided added value for differentiating malignant from benign ampullary strictures.