Complex pediatric cardiac disease is associated with brain impairment and neurodevelopmental disorders, particularly in patients requiring cardiac surgery for aortic arch anomalies. This study examines the incidence, risk factors, and outcomes of perioperative brain injury in children undergoing aortic arch repair who had aortic arch anomalies. A total of 145 children with aortic arch anomalies in our center undergoing aortic arch repair between January 2014 and December 2022 were enrolled. There were 129 (89.0%) with coarctation of the aorta (COA) and 16 (9.7%) with interrupted aortic arch (IAA). Risk factor analysis of brain injuries was done using perioperative imaging and included symptoms of hemorrhagic stroke, arterial ischemic stroke, white matter injury, cerebral sinus venous thrombosis, and other pathologies. Preoperatively, 50/145 (34.5%) patients had brain injuries. Multivariate analysis showed that an increased risk of hemorrhagic stroke was associated with newborns (odds ratio [OR], 2.09 [95% CI 0.08-3.50]), isolated COA (OR, 3.69 [95% CI 1.23-7.07]), mechanical ventilation (MV) ([OR, 2.56 [95% CI 1.25-4.03]), and sepsis (OR, 1.73 [95% CI 0.46-3.22]). Newborns ([OR, 1.91 [95% Cl 0.58-3.29]) and weight-for-age z score ([OR, -0.45 [95% CI -0.88 to -0.1]) were associated with an increased risk of white matter injury. New postoperative brain injuries were present in 12.9% of the patients (16/124). Deep hypothermic circulatory arrest (DHCA) was associated with new postoperative brain injuries compared with deep hypothermic low-flow (DHLF) plus antegrade cerebral perfusion (ACP) (([OR, 2.67 [95% CI, 0.58-5.75])). Isolated COA was almost associated with new postoperative brain injuries (OR, 1.13 [95% CI, -0.04 to 2.32]). Children diagnosed with isolated COA appeared to have a higher risk of perioperative brain injury, but the underlying mechanisms are still unclear. We focused on the intrinsic mechanism by which changes in hemodynamics caused by COA result in perioperative brain injury. Further research will be needed to optimize the personalized treatment and cerebral perfusion techniques for complex pediatric cardiac surgery.