Background: It is important to identify early predictors of functional limitations in children after congenital heart surgery to optimise their independence as they prepare for school. The purpose of this study is to determine potentially modifiable predictor variables of functional abilities in pre-school children who underwent complex cardiac surgery at 6 weeks of age or earlier. Methods: This prospective inception cohort study comprised a sample of 165 survivors (63% boys) who had complex cardiac surgery (75% biventricular repairs) at Stollery Children’s Hospital, Edmonton, Alberta. We excluded children with chromosomal abnormalities. When children were 4–5 years of age, the parents completed the Adaptive Behavioral Assessment System II. Regression analysis was used to assess the association between multiple risk factors and each of the four continuous composite scores. Results: The mean scores for the practical domain and general adaptive composite score of the Adaptive Behavioural Assessment System were lower than the conceptual and social domains, with 13.3% of the children having a delay in the practical domain. There was a significant association between the general adaptive (p=0.003; 0.012), conceptual (p=0.0004; 0.042), social (p=0.0007; 0.028), and the practical (p=0.046; 0.003) domain composite scores with the mother’s education and preoperative plasma lactate, respectively. Conclusion: Maternal education may be a marker for the social context of children, and warrants societal attention to improve functional outcomes. Preoperative lactate as a potentially modifiable variable may warrant increased attention to early diagnosis and aggressive resuscitation of young infants with congenital heart disease.