Abstract Objective To compare neurodevelopmental (ND) outcomes of preschool survivors of the Fontan procedure with those of children with congenital heart disease (CHD) undergoing biventricular (BV) repair and to investigate predictors of ND outcome for those with single ventricle (SV) CHD, including hypoplastic left heart syndrome (HLHS). Methods ND outcomes were assessed at 4 years of age including cognition, visual-motor integration, behavior, social skills and academic achievement. Unadjusted outcomes were compared between the BV and SV patients. Predictors of ND outcome were assessed in the SV patients. Multiple-covariate models were evaluated using patient-related, operative, and post-operative covariates. Results ND evaluation was performed in 365 children, 112 after the Fontan [HLHS (n = 91), other SV (n = 21)] and 253 after BV repair. Compared to BV patients, the SV patients performed worse in terms of processing speed, inattention and impulsivity. Otherwise there were no significant differences between the groups for any domain. There was a trend toward lower performance for SV patients on visual motor integration. Outcomes for patients with HLHS were not worse than for other forms of functional SV. Patient factors were more important predictors of ND outcomes than were operative management variables. Conclusions In this cohort, unadjusted ND outcomes for preschool survivors of the Fontan procedure are similar to those for children with CHD undergoing BV repair for most domains. Among the Fontan patients, HLHS was not associated with worse outcomes compared to other forms of SV.