Extracorporeal membrane oxygenation (ECMO) is lifesaving for many critically ill children with congenital heart disease (CHD). However, limited information is available about their ensuing neurodevelopmental (ND) outcomes. We describe early ND outcomes in a cohort of children supported with ECMO for cardiac indications. Twenty-eight patients supported with ECMO at age < 36 months underwent later ND testing at 12–42 months of age using the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III). ND scores were compared with normative means and with ND outcomes of a matched cohort of 79 children with CHD undergoing cardiac surgery but not requiring ECMO support. Risk factors for worse ND outcomes were identified using multivariable linear regression models. Cardiac ECMO patients had ND scores at least one standard deviation below the normative mean in the gross motor (61%), language (43%), and cognitive (29%) domains of the Bayley-III. Cardiac ECMO patients had lower scores on the motor, language, and cognitive domains as compared to the matched non-ECMO group and clinically important (1/2 SD) differences in the motor domain persisted after controlling for primary caregiver education and number of cardiac catheterizations. Risk factors of worse ND outcomes among cardiac ECMO patients in more than one developmental domain included older age at first cannulation and more cardiac catheterization and cardiac surgical procedures prior to ND assessment. Overall, children supported on ECMO for cardiac indications have significant developmental delays and warrant close ND follow-up.