Background: Acute kidney injury (AKI) is a common complication observed after neonatal aortic arch repair. We studied its incidence after procedures carried out using deep hypothermic circulatory arrest (DHCA) versus moderate hypothermia with distal aortic perfusion (MHDP), usually through the common femoral artery. In both groups, continuous regional cerebral perfusion (RCP) was used during the time required for aortic arch repair. Methods: A total of 125 neonates underwent aortic arch repair. Between 2007 and 2012, DHCA with RCP was used in 51 neonates. From 2013 to 2019, MHDP with RCP was performed on 74 newborns. Operative complexity was similar in both periods. Acute kidney injury was defined as a significant elevation of serum creatinine and was classified according to the neonatal modified n-KDIGO (neonatal Kidney Disease: Improving Global Outcomes) stages 1 to 3 (Kidney Disease Improving: Global Outcomes). Results: Acute kidney injury was observed in a total of 68 patients (68/125: 54.4%). In the majority (44/68: 64.7%), n-KDIGO stage 1 occurred. Stage 2 (n = 14) and stage 3 (n = 10) were observed more frequently after DHCA versus MHDP: 29.4% (15/51) versus 12.2% (9/74), P = .02. At cardiopulmonary bypass end, lactate levels were significantly higher ( P = .001) after DHCA: 3.4 (2.9-4.3) mmol/L compared to 2.7 (2.3-3.7) mmol/L after MHDP. Early mortality was 12% (15/125) in the entire cohort. It was 17.6% (9/51) after DHCA versus 8.1% (6/74) after MHDP, however not statistically significant ( P = .16). Conclusion: Mild (stage 1) AKI occurred frequently after neonatal aortic arch repair. The use of MHDP was associated with a significantly lower incidence of moderate (stage 2) and severe (stage 3) AKI forms.