Metallic and hyperdense artifacts and T1-shortening substances in the abdominal aortic aneurysm (AAA) sac generated by embolic materials and lipiodol pose challenges in the identification of endoleaks on follow-up computed tomography (CT) or magnetic resonance imaging (MRI). To evaluate the usefulness of contrast-enhanced subtraction MRI (CES-MRI) for detecting endoleaks after endovascular abdominal aortic aneurysm repair (EVAR) with intraoperative AAA sac embolization compared with CE-CT, this study was conducted. In this study, 28 consecutive patients who underwent EVAR with prophylactic AAA sac embolization were included. All patients underwent CES-MRI and CE-CT to detect endoleaks. The definitive diagnosis of endoleaks was a consensus reading of CE-CT and CES-MRI by two certified radiologists, in addition to angiography or reproducible radiological findings in the observational examination. Analysis was performed to evaluate which examination was better for detecting endoleaks. The sensitivity, specificity, and area under the curve of CE-CT and CES-MRI according to observer 1 were 50%, 100%, and 0.813 (95% confidence interval [CI] = 0.625-1.00) and 100%, 95%, and 0.997 (95% CI = 0.984-1.00), respectively, and those according to observer 2 were 50%, 100%, and 0.750 (95% CI = 0.514-0.986) and 100%, 95%, and 0.969 (95% CI = 0.903-1.00), respectively. Intolerable artifacts were significantly observed on CE-CT. The severity of the artifacts did not depend on the stent graft on CT and MRI. Although no significant difference was observed, CES-MRI tended to have better accuracy for endoleak detection in EVAR with intraoperative AAA sac embolization than CE-CT.