Adolescents with single ventricle heart disease (SVHD) exhibit mood and cognitive deficits, which may result from injury to the basal ganglia structures, including the caudate nuclei. However, the integrity of the caudate in SVHD adolescents is unclear. Our aim was to examine the global and regional caudate volumes, and evaluate the relationships between caudate volumes and cognitive and mood scores in SVHD and healthy adolescents. We acquired two high‐resolution T1‐weighted images from 23 SVHD and 37 controls using a 3.0‐Tesla MRI scanner, as well as assessed mood (Patient Health Questionnaire‐9 [PHQ‐9]; Beck Anxiety Inventory [BAI]) and cognition (Montreal Cognitive Assessment [MoCA]; Wide Range Assessment of Memory and Learning–2; General Memory Index [GMI]) functions. Both left and right caudate nuclei were outlined, which were then used to calculate and compare volumes between groups using ANCOVA (covariates: age, gender, and head‐size), as well as perform 3D surface morphometry. Partial correlations (covariates: age, gender, and head‐size) were used to examine associations between caudate volumes, cognition, and mood scores in SVHD and controls. SVHD subjects showed significantly higher PHQ‐9 and BAI scores, indicating more depressive and anxiety symptoms, as well as reduced GMI scores, suggesting impaired cognition, compared to controls. SVHD patients showed significantly reduced caudate volumes (left, 3,198.8 ± 490.1 vs. 3,605.0 ± 480.4 mm3, p < 0.004; right, 3,162.1 ± 475.4 vs. 3,504.8 ± 465.9 mm3, p < 0.011) over controls, and changes were localized in the rostral, mid‐dorsolateral, and caudal areas. Significant negative correlations emerged between caudate volumes with PHQ‐9 and BAI scores and positive correlations with GMI and MoCA scores in SVHD and controls. SVHD adolescents show significantly reduced caudate volumes, especially in sites that have projections to regulate mood and cognition, which may result from developmental and/or hypoxia‐/ischemia‐induced processes.