Background: Brain injury, impaired brain maturation, and long-term neurodevelopmental disorders are common in infants with congenital heart diseases (CHD). We aimed to assess whether plasma glial fibrillary acidic protein (GFAP) can predict neurodevelopmental anomalies in CHD infants operated on cardiopulmonary bypass (CPB). Methods: We measured plasma GFAP in 38 infants at multiple CPB phases. Cognitive, neuropsychological, and psychopathological functioning were assessed 5.7 ± 2.2 years after surgery. We identified an impaired global neurodevelopmental index (NDI) when at least two domains were abnormal. The relationships between NDI, GFAP, and clinical variables were explored with non-supervised feature selection methods and modeled with a nested non-linear logistic regression. Results: Intelligence quotient scores were within the normal range in 84% of children, whereas 58% showed an abnormal NDI, with the greatest impairments in the psychopathological area. The plasma GFAP peak was 0.95 (0.44–1.57) ng/mL, and it was correlated with age, weight, duration of surgery phases, and CPB minimum temperature. In the regression model, the GFAP peak was associated with an impaired NDI with a possible flexible point toward NDI impairment at 0.49 ng/mL, keeping constant ICU stay, CPB duration, CHD anatomy, weight, and CPB minimum temperature. Conclusion: GFAP is a promising early marker of abnormal long-term neuropsychological development.