Prenatal diagnosis of congenital anomalies of the kidney and urinary tract (CAKUT) is crucial for providing appropriate counseling regarding potential postnatal outcomes. While ultrasound (US) remains the gold standard for diagnosing CAKUT, magnetic resonance imaging (MRI) has gained traction for assessing complex congenital anomalies. However, the diagnostic accuracy of fetal MRI for CAKUT has not been thoroughly evaluated. This study aimed to compare the effectiveness of prenatal US and MRI in diagnosing CAKUT. We retrospectively reviewed the cases of pregnant mothers evaluated with both imaging modalities at a tertiary fetal care center from 2012 to 2020. Data collection included maternal demographics, prenatal imaging results, and postnatal diagnoses. We categorized the imaging findings into kidney, ureteral, and bladder anomalies and assessed their concordance with postnatal diagnoses. The diagnostic accuracy of prenatal MRI and US was evaluated using sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Our analysis identified 33 fetuses meeting the inclusion criteria. The results revealed that prenatal MRI had significantly lower rates of incomplete results compared to US (6.7% vs. 12.1%, p<0.001). Furthermore, fetal MRI exhibited greater sensitivity and NPV for identifying anomalies than US (0.96 vs. 0.87 and 0.98 vs. 0.93, respectively), while showing lower specificity and PPV (0.91 vs. 0.95 and 0.85 vs. 0.91, respectively). Notably, MRI demonstrated higher sensitivity, PPV, and NPV for kidney anomalies, while both imaging modalities yielded equivalent results for bladder anomalies. Although these findings trended towards significance, they did not reach statistical significance. Nonetheless, the results suggest that fetal MRI should be regarded as a complementary tool to fetal US, particularly for evaluating kidney and ureteral anomalies, with ongoing research aimed at validating these findings in larger cohorts.