Being overweight is associated with reduced functional capacity in Fontan patients. Increased adiposity leads to accumulation of epicardial and intra-abdominal visceral fat, which produce proinflammatory cytokines and may affect endothelial function. This retrospective study to evaluate the association between visceral fat and Fontan haemodynamics included 23 Fontan patients >18 years old with MRI and catheterization data available. Epicardial fat volume indexed to body surface area was measured by cardiac MRI, and intra-abdominal visceral fat thickness and subcutaneous fat thickness were derived from abdominal MRI. Stepwise regression models were used to determine univariable and multivariable associations between fat measures and haemodynamics. Mean age was 28.2 ± 9.5 years and body mass index was 26 ± 4 kg/m2. Mean central venous pressure was 13 ± 3 mmHg and pulmonary vascular resistance index was 1.23WU·m2 (interquartile range: 0.95–1.56). Epicardial fat volume was associated with age (r2 = 0.37, p = 0.002), weight (r2 = 0.26, p = 0.013), body mass index (r2 = 0.27, p = 0.011), and intra-abdominal visceral fat (r2 = 0.30, p = 0.018). Subcutaneous fat thickness did not relate to these measures. There was modest correlation between epicardial fat volume and pulmonary vascular resistance (r2 = 0.27, p = 0.02) and a trend towards significant correlation between intra-abdominal fat thickness and pulmonary vascular resistance (r2 = 0.21, p = 0.06). Subcutaneous fat thickness was not associated with Fontan haemodynamics. In multivariable analysis, including age and visceral fat measures, epicardial fat was independently correlated with pulmonary vascular resistance (point estimate 0.13 ± 0.05 per 10 ml/m2 increase, p = 0.03). In conclusion, in adults with Fontan circulation, increased visceral fat is associated with higher pulmonary vascular resistance. Excess visceral fat may represent a therapeutic target to improve Fontan haemodynamics.