Abstract Aims Effective therapy to improve exercise capacity in Fontan patients is lacking. Leg-focused high-weight resistance training might augment the peripheral muscle pump and thereby improve exercise capacity. Methods and results This randomized semi-cross-over controlled trial investigated the effects of a 12-week leg-focused high-weight resistance training plus high-protein diet, on (sub)maximal exercise capacity, cardiac function (assessed with cardiovascular magnetic resonance), muscle strength, and quality of life in paediatric Fontan patients. Twenty-eight paediatric Fontan patients were included, 27 patients, (median age 12.9 10.5–15.7), and successfully completed the programme. Peak oxygen uptake (PeakVO2) at baseline was reduced 33.3 mL/kg/min (27.1–37.4), 73% (62–79) of predicted. After training PeakVO2/kg and Peak workload improved significantly with +6.2 mL/kg/min (95%CI: 3.4–9.0) (+18%) P < 0.001 and +22 Watts (95%CI: 12–32) (+18%) P < 0.001, respectively, compared to the control period. Indexed single ventricle stroke volume increased significantly 43 mL/beat/m2 (40–49) vs. 46 (41–53), P = 0.014, as did inferior vena cava flow 21 mL/beat/m2 (18–24) vs. 23 (20–28), P = 0.015, while superior vena cava flow remained unchanged. The strength of all measured leg-muscles increased significantly compared to the control period. Self-reported quality of life improved on the physical functioning and change in health domains of the child health questionnaire, parent-reported quality of life improved the bodily pain, general health perception, and change in health domains compared to the control period. Conclusion In a relatively large group of 27 older Fontan children, 12-weeks of leg-focused high-weight resistance training improved exercise capacity, stroke volume, (sub)maximal exercise capacity, muscle strength, and domains of quality of life. Registration International Clinical Trials: Trial NL8181. Lay Summary Is leg-focused high-weight resistance training an effective therapy to improve reduced exercise capacity in patients with a Fontan circulation? Key Finding: Twelve weeks of leg-focused high-weight resistance training in children with a Fontan circulation improved exercise capacity, single ventricular stroke volume, (sub)maximal exercise capacity, muscle strength, and physical domains of quality of life. Take-home Message: Leg-focused high-weight resistance training results in improved exercise capacity, cardiac function, and quality of life patients with a Fontan circulation. Patients with a Fontan circulation should be motivated to perform lower limb strengthening exercises. Graphical Abstract Graphical Abstract