We evaluated the effects of different respiratory assist modes on cerebral blood flow (CBF) and arterial oxygenation in single-ventricle patients after bidirectional superior cavopulmonary anastomosis (BCPA). We hypothesized that preserved auto-regulation of respiration during neurally adjusted ventilatory assist (NAVA) may have potential advantages for CBF and pulmonary blood flow regulation after the BCPA procedure. We enrolled 23 patients scheduled for BCPA, who underwent pressure-controlled ventilation (PCV), pressure support ventilation (PSV), and NAVA at two assist levels for all modes in a randomized order. PCV targeting large V _T (15 mL × kg⁻¹) resulted in lower CBF and oxygenation compared to targeting low V _T (10 mL × kg⁻¹). During PSV and NAVA, ventilation assist levels were titrated to reduce EAdi from baseline by 75 % (high assist) and 50 % (low assist). High assist levels during PSV (PSV_high) were associated with lower PaCO₂, PaO₂, and O₂SAT, lower CBF, and higher pulsatility index compared with those during NAVA_high. There were no differences in parameters when using low assist levels, except for slightly greater oxygenation in the NAVA_low group. Modifying assist levels during NAVA did not influence hemodynamics, cerebral perfusion, or gas exchange. Targeting the larger V _T during PCV resulted in hyperventilation, did not improve oxygenation, and was accompanied by reduced CBF. Similarly, high assist levels during PSV led to mild hyperventilation, resulting in reduced CBF. NAVA’s results were independent of the assist level chosen, causing normalized PaCO₂, improved oxygenation, and better CBF than did any other mode, with the exception of PSV at low assist levels.