Purpose To compare the accuracy of magnetic resonance (MR) imaging with that of computed tomography (CT) for the diagnosis of acute appendicitis in emergency department (ED) patients. Materials and Methods This was an institutional review board-approved, prospective, observational study of ED patients at an academic medical center (February 2012 to August 2014). Eligible patients were nonpregnant and 12- year-old or older patients in whom a CT study had been ordered for evaluation for appendicitis. After informed consent was obtained, CT and MR imaging (with non-contrast material-enhanced, diffusion-weighted, and intravenous contrast-enhanced sequences) were performed in tandem, and the images were subsequently retrospectively interpreted in random order by three abdominal radiologists who were blinded to the patients' clinical outcomes. Likelihood of appendicitis was rated on a five-point scale for both CT and MR imaging. A composite reference standard of surgical and histopathologic results and clinical follow-up was used, arbitrated by an expert panel of three investigators. Test characteristics were calculated and reported as point estimates with 95% confidence intervals (CIs). Results Analysis included images of 198 patients (114 women [58%]; mean age, 31.6 years ± 14.2 [range, 12-81 years]; prevalence of appendicitis, 32.3%). The sensitivity and specificity were 96.9% (95% CI: 88.2%, 99.5%) and 81.3% (95% CI: 73.5%, 87.3%) for MR imaging and 98.4% (95% CI: 90.5%, 99.9%) and 89.6% (95% CI: 82.8%, 94.0%) for CT, respectively, when a cutoff point of 3 or higher was used. The positive and negative likelihood ratios were 5.2 (95% CI: 3.7, 7.7) and 0.04 (95% CI: 0, 0.11) for MR imaging and 9.4 (95% CI: 5.9, 16.4) and 0.02 (95% CI: 0.00, 0.06) for CT, respectively. Receiver operating characteristic curve analysis demonstrated that the optimal cutoff point to maximize accuracy was 4 or higher, at which point there was no difference between MR imaging and CT. Conclusion The diagnostic accuracy of MR imaging was similar to that of CT for the diagnosis of acute appendicitis.