Background: The S100 calcium-binding protein β (S-100β) and the neuron-specific enolase (NSE) can reflect brain injury, the value of the perioperative changes in S-100β and NSE levels in children with end-stage liver disease (ESLD) undergoing parent liver transplantation is unknown. This was to investigate the effects of parent liver transplantation on the changes of serum NSE and S-100β during the perioperative period, on brain injury, and on postoperative cognitive function. Methods: This was a prospective observational study of infants with congenital biliary atresia who had to undergo selective liver transplantation in 2017 at Tianjin First Central Hospital. Blood samples were drawn before skin incision (T1), 30 min after anhepatic phase (T2), 1 h of neohepatic phase (T3), and 24 h after hepato-reperfusion (T4). S-100β and NSE were measured by ELISA. Children were assessed using the Bayley Scale of Infant Development (BSID) 1 day before and 3 months after surgery. The pediatric anesthesia emergence delirium (PAED) was used at 0.5, 2, and 4 h after extubation. Results: Compared with T1, serum NSE and S100β were increased at T2, T3, and T4. Compared with T1, serum S-100β and NSE increased at T2 and peaked at T3 (all P<0.05). S-100β and NSE decreased at T4 (both P<0.05). Compared with 1 day before surgery, MDI and PDI were decreased at 3 months after surgery (MDI: from 87.7±8.4 to 84.5±8.5, P=0.015; PDI: from 82.9±8.7 to 79.6±8.8, P=0.016). Conclusion: Liver transplantation causes a certain degree of brain injury in children, as revealed by serum NSE and S100β levels.