Adolescents and young adults (AYAs) with congenital heart disease (CHD) experience cognitive difficulties that may be related to functional brain differences. This study investigated relationships between resting-state functional connectivity and executive function (EF) outcomes AYAs with CHD compared to healthy controls, utilizing a data-driven approach, and questionnaire- and performance-based measures of EF. This study also elucidated whether CHD severity impacts the strength or direction of brain-behavior relationships, by looking at single-ventricle and two-ventricle CHD separately. CHD individuals showed significantly and clinically elevated EF difficulties, with single-ventricle CHD showing increased impairments. Results showed overall decreased connectivity in CHD compared to controls. In the single-ventricle CHD group only, decreased connectivity within the cognitive control domain and between the cognitive control and default mode domains explained planning and organization difficulties. Findings suggest that functional brain differences help explain challenges with complex EF abilities in AYAs with CHD, especially in individuals with greater severity.