Neurodevelopmental disabilities are common in infants with critical congenital heart disease (CCHD). A prospective, longitudinal cohort study was conducted to establish the prevalence and early determinants of adverse motor outcomes in infants who underwent cardiac surgery with cardiopulmonary bypass before six months of age. Motor development was assessed in 147 preschoolers using the Movement Assessment Battery for children-II. Although the majority displayed an average motor development, 22% of preschool children with CCHD deteriorated in their motor developmental score compared to their previous assessment at 18 months, especially in those with an aortic arch anomaly (AAA) (35%). Individual stability over time appeared to be moderate and the number of children with a motor delay increased, up to 20% in children with AAA. Motor development up to 42 months was best predicted by gestational age, cardio pulmonary bypass time, aortic cross clamp time, number of heart catheterizations up to 18 months and early motor outcomes. The increase in number of preschool children with a motor delay underlines the importance of longitudinal screening of motor skills in children with CCHD at risk for adverse motor outcomes. Offering early interventions may protect their current and future cardiovascular health as motor development is an independent predictor of exercise capacity, physical activity and participation in daily living.