To assess health-related quality of life (HRQOL) and global quality of life (QOL) in children and adolescents with Fontan physiology and identify key predictors influencing these outcomes. Cross-sectional analysis of 73 children and adolescents enrolled in the Australia and New Zealand Fontan Registry aged 6-17years, at least 12months post-Fontan operation. Assessments included the Pediatric Quality of Life Inventory (PedsQL) for HRQOL and a developmentally-tailored visual analogue scale (0-10) for global QOL, along with validated sociodemographic, clinical, psychological, relational, and parental measures. Clinical data were provided by the Australia and New Zealand Fontan Registry. Participants (mean age: 11.5±2.6years, 62% male) reported lower overall HRQOL (P<.001), and lower scores across all HRQOL domains (all P<.0001), compared with normative data. Median global QOL score was 7.0 (IQR 5.8-8.0), with most participants (79%) rating their global QOL ≥6. Anxiety and depressive symptoms requiring clinical assessment were reported by 21% and 26% of participants, respectively. Age, sex, and perceived seriousness of congenital heart disease explained 15% of the variation in HRQOL scores, while depressive symptoms and treatment-related anxiety explained an additional 37% (final model: 52% of variance explained). For global QOL, sociodemographic and clinical factors explained 13% of the variance in scores, while depressive symptoms explained a further 25% (final model: 38% of variance explained). Parental factors were not associated with child QOL outcomes. Children and adolescents with Fontan physiology experience lower HRQOL than community-based norms, despite reporting fair overall QOL. Psychological factors predominantly influenced QOL outcomes, indicating strategies to bolster psychological health could improve QOL in this population.