To assess atrial function in Fontan patients using cardiac MRI (CMR) and determine the relationships between atrial function, hemodynamics, and clinical outcomes. Two center chart review identified all Fontan patients with technically adequate CMR to assess atrial function within 1 year of cardiac catheterization and age-matched controls with CMR. Atrial reservoir, conduit, and pump global longitudinal strain and strain rate measurements were determined by CMR. Univariate and stepwise multivariable analysis were conducted to detect associations of atrial function measures with ventricular end diastolic pressure (EDP), cardiac index (CI), exercise capacity, liver stiffness and a composite outcome of heart transplantation, ventricular assist device or death. The study cohort was comprised of 33 Fontan patients and 30 age-matched controls. Fontan patients had lower atrial reservoir and conduit strain, and lower reservoir, conduit, and pump strain rate compared to age-matched controls. Atrial conduit strain was negatively associated with EDP and lower atrial pump-to-conduit strain ratio was associated with lower cardiac index in multivariable analysis. Lower atrial pump strain was associated with lower exercise capacity (per 1% increase: β = 2.3 ± 0.9, p = 0.03) and higher liver stiffness (per 1% increase: β =  − 0.12 ± 0.03, p = 0.002). Higher atrial pump strain (HR per 1% increase = 0.53 [95% confidence interval 0.22, 0.83], p = 0.002) and ventricular ejection fraction (HR per 1% increase = 0.90 [95% confidence interval 0.80, 0.98], p = 0.02) were associated with lower risk for the composite adverse outcome. Atrial function is impaired in Fontan patients and is associated with worse CI, EDP, exercise performance, liver stiffness, and a higher risk for adverse outcomes.