Peak oxygen consumption and anaerobic threshold are both decreased in patients with a Fontan-type circulation. This study wanted to evaluate oxygen uptake kinetics at the onset and at the end of of a steady-state low-level exercise. The delay in cardiorespiratory response was evaluated by calculating the oxygen deficit at the onset of exercise and the recovery half-time at the end. Twelve patients with Fontan circulation (aged 11.4 − SD 5.1 year; 5.2 − 1.9 year after surgery) and 26 normal controls of comparable age (11.3 − 2.2 year) were submitted to a constant-load exercise test of six minutes on a treadmill (speed 5 km/h, inclination 4%). Gas exchange was measured using a breath-by-breath technique. The normalized oxygen deficit was calculated by subtracting the oxygen uptake (VO2) values measured at the onset of exercise from the steady-state VO2 obtained at the end of exercise. These differences were cumulated and expressed as a percentage of the cumulated oxygen cost for the 6 min exercise test. The half-time recovery time was defined as the time to reach 50% of the end exercise VO2 value. The normalized oxygen deficit was significantly higher in Fontan-patients compared to the control group (10.2 − 4.6% vs. 6.1 − 1.3%; p < .001). Also the recovery half-time was significantly higher in the patient group compared to the control group (74.2 − 25.6 s vs. 51.2 − 10.8 s; p < .05). A blunted heart rate response was present in the patients during the first two minutes of exercise, indicating that a slowed cardiac output response could explain the decreased oxygen kinetics in Fontan-patients.