During pediatric cardiac surgery with cardiopulmonary bypass (CPB) for congenital heart disease, systemic hemodynamics dramatically change, which also causes changes in the cerebral hemodynamics. One of the representative methods in bedside monitoring for the estimation of cerebral hemodynamics during pediatric cardiac surgery is transcranial Doppler ultrasonography (TCD). However, there seem to be few reports on the changes in TCD findings in such operations, especially in cyanotic children. Accordingly, we examined the changes in TCD indices during these procedures in cyanotic children as well as non-cyanotic children. In the post hoc analysis of a previous prospective observational study, TCD indices of the middle cerebral artery at the start and end of surgery in patients aged 6 years or less were compared. The cerebral oxygenation (rSO₂) values were also compared. For this study, 47 cyanotic children and 49 non-cyanotic children were evaluated. At the end of surgery, cerebral blood flow velocities decreased and cerebrovascular resistance increased significantly compared to the start of surgery in both the cyanotic and non-cyanotic patients. This finding was almost constant regardless of age differences, although cerebral blood flow velocities and the rSO₂ increased until around 20 months after birth. The rSO₂ values did not change between the start and end of surgery. Thus, the changes in cerebral hemodynamics during pediatric surgery with CPB in cyanotic children were not so different from those in non-cyanotic children. The significance of monitoring of cerebral hemodynamics by TCD and rSO₂ should be evaluated further.