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Introduction Behavioral outcomes may be suboptimal in school-age children and adolescents with congenital heart disease (CHD). However, little is known about the behavioral outcomes of preschool children with CHD. This study aimed to compare behavioural outcomes in preschool children with CHD and controls, and to investigate the impact of a cognitively stimulating home environment on these outcomes. Methods Cross-sectional case-control study based on parent-rated questionnaires assessing child behavior and cognitively stimulating opportunities in the home environment in 56 preschool children (4–6 years) with CHD and 215 control participants. Validated questionnaires were used to assess temperament (Child Behavior Questionnaire), autism traits (Social Communication Questionnaire), ADHD symptoms (ADHD-Rating Scale-IV), empathy (EmQue), and behavioral difficulties (Strengths and Difficulties Questionnaire). Higher scores on these measures indicate more severe difficulties. The Cognitively Stimulating Parenting Scale was used to assess the presence of cognitive stimulating opportunities in the home environment. Results Univariate robust regression analyses showed that children with CHD compared to controls had higher levels of age-adjusted hyperactivity/impulsivity (B = −0.339, p = 0.032), hyperactivity/inattention (B = −0.390, p = 0.032) and peer relationship problems (B = −0.298, p = 0.045), after controlling for gestational age at birth, sex and neighborhood deprivation, with results surviving false discovery rate correction. We did not find any differences between children with CHD and controls in the other behavioral measures assessed. Group (CHD or control) significantly moderated the relationship between cognitively stimulating opportunities at home and selective behavioral outcomes: hyperactivity/impulsivity, inattention and peer problems. More cognitively stimulating opportunities at home were associated with more favorable behavioral outcomes in children with CHD (hyperactivity/impulsivity: B = −0.092, p < 0.001; hyperactivity/inattention: B = −0.088, p < 0.001; peer problems: B = −0.124, p < 0.001) but not in controls (hyperactivity/impulsivity: B = −0.005, p = 0.727; hyperactivity/inattention: B = −0.019, p = 0.225; peer problems: B = −0.002, p = 0.911). Conclusions Compared to controls, and after adjusting for potential confounders, preschool children with CHD have more hyperactivity/impulsivity, inattention and peer relationship problems. Fewer behavioral problems were associated with a more cognitively stimulating home environment, highlighting this modifiable factor as a promising target for future longitudinal research.