Fenestration in the Fontan circulation potentially liberates patients from factors leading to cardiovascular remodelling, through stable haemodynamics with attenuated venous congestion. We hypothesised that a fenestrated Fontan procedure would possess chronic haemodynamic advantages beyond the preload preservation. We enrolled 35 patients with fenestrated Fontan with a constructed pressure-volume relationship under dobutamine (DOB) infusion and/or transient fenestration occlusion (TFO). Despite the use of antiplatelets and anticoagulants, natural closure of fenestration was confirmed in 11 patients. Cardiovascular properties in patients with patent fenestration (P-F) were compared with those in patients with naturally closed fenestration (NC-F). To further delineate the roles of fenestration, paired analysis in patients with P-F was performed under DOB or rapid atrial pacing with/without TFO. As compared with P-F, patients with NC-F had a higher heart rate (HR), smaller ventricular end-diastolic area, better ejection fraction and higher central venous pressure, with higher pulmonary resistance. While this was similarly observed after DOB infusion, DOB markedly augmented diastolic and systolic ventricular stiffness in patients with NC-F compared with patients with P-F. As a mirror image of the relationship between patients with P-F and NC-F, TFO markedly reduced preload, suppressed cardiac output, and augmented afterload and diastolic stiffness. Importantly, rapid atrial pacing compromised these haemodynamic advantages of fenestration. As compared with patients with NC-F, patients with P-F had robust haemodynamics with secured preload reserve, reduced afterload and a suppressed beta-adrenergic response, along with a lower HR at baseline, although these advantages had been overshadowed, or worsened, by an increased HR.