Objective To evaluate the performance of contrast-enhanced mammography (CEM) compared to magnetic resonance imaging (MRI) for estimating residual tumor size after neoadjuvant chemotherapy (NAC) in women with newly diagnosed breast cancer. Methods The institutional review board approved this study. This prospective study included women with newly diagnosed breast cancer who underwent breast CEM and MRI at the end of the last cycle of NAC and before definitive surgery. Size of residual malignancy on post-NAC CEM and MRI was compared with surgical pathology. Agreements and correlations of CEM and MRI measurements with histological size were assessed. Results Thirty-three patients were included with a mean age of 45 years (range 22–76). The sensitivity, specificity, and positive and negative predictive value for detection of residual disease of CEM were 76%, 87.5%, 95%, and 86.4%, and those of MRI were 92%, 75%, 92%, and 75%. Comparing CEM to MRI, the mean difference was −0.8 cm, concordance coefficient was 0.7, and Pearson correlation was 0.7 (p = 0.0003). The concordance coefficient between measurements of each imaging modality and pathologic tumor size was 0.7 for CEM and 0.4 for MRI. Pearson correlation was 0.8 for CEM and 0.5 for MRI. Mean differences between CEM, MRI, and residual histopathological tumor size were 0.8 cm and 1.8 cm, respectively. Conclusions CEM has good correlation and agreement with histopathology for measuring residual disease after NAC. CEM was comparable to MRI, showing high positive predictive value and specificity for detecting residual disease.