Recently, it is common to perform the Fontan procedure after the Glenn procedure as surgical repair for the univentricular heart. How the brain oxygen saturation (rSO₂) values change with the cardiac restoration and the process of growth during these procedures in individual children remains unknown. In this study, we retrospectively studied rSO₂ data as well as the perioperative clinical records of 30 children who underwent both Glenn and Fontan procedures by the same surgeon in the same institute. The rSO₂ was measured at the beginning and end of each procedure with an INVOS 5100C. Cerebral perfusion pressure was calculated by subtracting central venous pressure from mean arterial pressure. Arterial oxygen saturation (SaO₂) and the hemoglobin concentration were obtained as candidates affecting rSO₂ changes at the start and the end of both procedures. The rSO₂ increased during the Glenn procedure, but this increase was slight and insignificant. On the other hand, the rSO₂ significantly increased during the Fontan procedure. Significant increases in SaO₂ were observed only between the beginning and end of the Fontan procedure. Correlation coefficients determined by linear regression analysis were more than 0.5 between rSO₂ and SaO₂ in both procedures. Multiple linear regression analysis showed that SaO₂ was the key determinant of the rSO₂. The rSO₂ increases step by step from the Glenn to the Fontan procedure in the same patient. Within each procedure, SaO₂ is the key determinant of the rSO₂. The significance of rSO₂ monitoring in these procedures should be further evaluated.