Background: Neonatal aortic arch surgery remains one of the most challenging procedures in congenital cardiac surgery. In recent years, there has been a trend away from selective cerebral perfusion (SCP) and arrest of body circulation towards whole-body perfusion (WBP), a combination of SCP and lower-body perfusion (LBP), to facilitate arch surgery and preserve organ function. Methods: Retrospective, single-centre analysis was conducted of patients under one year of age undergoing aortic arch surgery from January 2014 until December 2022. SCP was used from January 2014-December 2017; WBP was implemented from January 2017-December 2022. Patients were separated according to the type of perfusion used during surgery, SCP or WBP. The cohort consisted of a total of 95 patients, 34 in the SCP group and 61 in the WBP group. Results: Patients in the WBP group showed significantly lower rates of intraoperative transfusions, namely red blood cells, fresh-frozen plasma and thrombocytes (p-value < 0.01, <0.01, and <0.01, respectively). The WBP group showed significantly lower creatinine and higher urine output values 24 and 72 h after surgery (p-value = 0.02, <0.01, respectively). The WBP group showed a significant lower incidence of major neurological complications (p-value 0.01). Binary logistic regression analyses showed favourable outcomes for the WBP group regarding 30-day mortality (OR = 0.03, CI = 0.003-0.391, p-value = <0.01), multiorgan failure (OR = 0.002, CI = 0-0.275, p-value = 0.01), neurological complications (OR = 0.994, CI = 0.998-1, p-value = 0.06) and postoperative renal replacement therapy (RRT) (OR = 0.989, CI = 0.983-0.995, p-value = <0.01). Conclusions: Patients with WBP received fewer intraoperative transfusions, showed improved postoperative renal function and suffered significantly fewer neurological complications.