The increasing complexity of congenital cardiac surgery has led to greater utilization of extracorporeal membrane oxygenation (ECMO) support for children post-surgery. This study aims to identify risk factors for mortality and brain injury in pediatric patients requiring post-cardiotomy ECMO and to evaluate their neurological outcomes. This retrospective study includes pediatric patients with congenital heart diseases who required ECMO after surgery. Risk factors for in-hospital mortality and brain injury were assessed. Neurodevelopmental status was determined using the Pediatric Cerebral Performance Category (PCPC) Scale at discharge and during follow-up. Between October 2014 and May 2021, 2651 pediatric patients underwent cardiac surgery, with 90 (3.4%) requiring ECMO. The mean age was 0.6 years, ranging from 1 day to 13 years and 7 months. ECMO was implemented for 45 patients due to CPB weaning failure (NW-CPB), 24 due to postoperative low-cardiac output syndrome (LCOS), and 21 for extracorporeal cardiopulmonary resuscitation (E-CPR). ECMO weaning was achieved in 73 patients (81%), with an overall mortality rate of 36%. Pre-implant lactate levels (OR: 1.13, 95% CI: 1.03-1.25; p = 0.009) and peak bilirubin levels (OR: 1.04, 95% CI: 0.87-1.24; p = 0.69) were risk factors for in-hospital mortality. Survival rates were 79% for LCOS, 60% for NW-CPB, and 48% for E-CPR. Brain injury incidence was 33%, with E-CPR being a significant risk factor (p = 0.006) and NW-CPB being protective (p = 0.001). Follow-up in November 2023 showed significant improvement in neurodevelopmental status (p < 0.001). Elevated pre-implant lactate and elevated bilirubin levels during ECMO are major risk factors for mortality. E-CPR is the primary risk factor for brain injury. Follow-up revealed significant improvements in neurodevelopmental outcomes.