Introduction: The aim of this study was to determine whether whole-body perfusion (WBP) consisting of a combined antegrade cerebral perfusion (ACP) and lower body perfusion (LBP) improves the outcome after aortic arch reconstruction surgery in neonates compared with ACP. Methods: Sixty-five consecutive patients under one year of age who underwent aortic arch reconstruction as the main procedure or as part of a more complex surgery from 2014-2020 in our center were included. The patients were separated into two groups, according to the perfusion strategy, either ACP (34 patients) as the control group or WBP (31 patients) as the intervention group. LBP was achieved through an arterial sheath in the femoral artery. Outcome parameters were postoperative renal, gastrointestinal, and neurological complications and 30-day mortality. Results: The patients in the WBP group showed lower intraoperative lactate levels and close to normal early postoperative renal and hepatic enzymes and LDH at PICU admission compared with the patients in the ACP group. The number of patients suffering from postoperative neurological complications and multiorgan failure was lower in the WBP group. Conclusion: In our experience, the combined use of ACP and LBP through the femoral artery showed an improvement, regarding postoperative neurologic complications in neonates and infants undergoing aortic arch surgery.