Symptoms of Crohn’s disease (CD) can be due to active inflammation or fibrosis. Differentiating these based on clinical presentation, endoscopy, laboratory parameters, and clinical scoring methods can be inaccurate and/or invasive. As therapy decisions are often directed based on whether active disease or fibrosis is present, a reliable and non-invasive test to distinguish these two etiologies would be a powerful clinical tool. CT enterography (CT-E) and MR enterography (MR-E) are two non-invasive imaging modalities tailored to evaluate the small bowel. The purpose of our study was to compare the ability of MR-E and CT-E to assess for active inflammation and mural fibrosis in patients with known CD as compared to a histologic reference standard. After obtaining MR-E and CT-E on the same day, a total of 61 histologic samples were obtained from twelve subjects aged 12–20 years via full-thickness bowel resection or endoscopy. These were evaluated by the pathologist for active inflammation and fibrosis. We found that while CT-E and MR-E were similar in their accuracies of depicting active inflammation, MR-E was significantly more sensitive in detecting fibrosis. Because of this and the lack of ionizing radiation from MR-E, we believe that MR-E rather than CT-E should serve as the primary imaging modality for the assessment of CD pediatric patients with non-acute clinical exacerbations.