Background: Improving surgical and interventional modalities for treating congenital heart disease has increased these children’s life expectancy, leading to increased cognitive and behavioral problems. Objectives: This study compared executive function between surgically and interventionally treated congenital heart disease children and their age-matched controls. Methods: In this retrospective cross-sectional study, we enrolled 30 children treated with surgery, 30 interventionally treated patients, and 30 healthy controls. These participants were compared in the executive function domains by the Stroop test, trail making test, cancellation test, visual and auditory memory span test, and behavioral problems using the parental form of strengths and difficulties questionnaire. Results: Executive function in memory span and sustained attention was lower in the surgical group than in the intervention group (P < 0.05). Both groups had lower flexibility, memory recall, simple and complex working memory, visual attention, and simple and complex selective attention performance (P < 0.05). The effect of behavioral problems on daily life was higher in surgical patients than in the intervention group (P < 0.0001). Both groups of patients had higher emotional, conduct, and communication problems than the control group (P < 0.0001). Conclusions: Interventionally treated patients had better performance than surgically treated patients. Regardless of disease severity or treatment, patients with congenital heart disease had poor performance than normal subjects and suffered from behavioral disorders affecting their daily lives. Therefore, it is essential to include diagnostic and therapeutic interventions for treating these patients’ executive function and behavioral problems.