(1) Background: Cerebral MRI plays a significant role in assessing the extent of brain injury in neonates with neonatal encephalopathy after perinatal asphyxia. Over the last decades, several MRI scoring systems were developed to enhance the predictive accuracy of MRI. The aim of this study was to validate the correlation of four established MRI scoring systems with cognitive long-term outcomes in cooled asphyxiated newborns. (2) Methods: Forty neonates with neonatal encephalopathy treated with therapeutic hypothermia were included in this retrospective study. The MRI scans from the second week of life were scored using four existing MRI scoring systems (Barkovich, NICHD, Rutherford, and Weeke). The patients' outcome was assessed with the Bayley Scales of Infant Development (BSID-III) at the age of 2 years. To evaluate the correlation between the MRI scoring system with the cognitive scores of BSID-III, the correlation coefficient was calculated for each scoring system. (3) Results: All four MRI scoring systems showed a significant correlation with the cognitive scores of BSID-III. The strongest correlation was found between the Weeke Score (r2 = 0.43), followed by the Rutherford score (r2 = 0.39), the NICHD score (r2 = 0.22), and the Barkovich score (r2 = 0.17). (4) Conclusion: Our study confirms previously published results in an independent cohort and indicates that the Weeke and Rutherford scores have the strongest correlation with the cognitive score of BSID-III in cooled asphyxiated newborns.