Near-infrared spectroscopy is routinely used in the monitoring of cerebral regional oxygen saturation (crSO₂) in neonates following congenital heart surgery. Decreased postoperative crSO₂ variability in these patients is associated with worse clinical outcomes, including neurodevelopmental outcomes. We sought to explore changes in crSO₂ variability between the preoperative and postoperative periods and associations with short-term clinical outcomes in neonates undergoing cardiac surgery. We performed a prospective cohort study of neonates undergoing cardiac surgery with cardiopulmonary bypass between November 2019 and May 2021. We calculated crSO₂ variability using averaged 1 min of crSO₂ values for a minimum of 12 h before, and the first 48 h following surgery. 37 neonates (median age at start of monitoring 4 days (interquartile range 2–5 days)) were included in our study. We observed a 30% decrease in crSO₂ variability between the preoperative and postoperative monitoring periods (p < 0.001). Preoperative crSO₂ variability increased by 9% (p = 0.009) for each additional postnatal day. There were no associations between the degree of decrease in crSO₂ variability postoperatively and class of cardiac lesion (e.g., aortic arch obstruction, single ventricle physiology) or short-term postoperative clinical outcomes. There was a significant decrease in postoperative crSO₂ variability following neonatal cardiac surgery as compared to the preoperative period, likely influenced by several factors. The impact of interventions on crSO₂ variability and resultant influence on long-term outcomes, such as neurodevelopmental outcomes, requires further exploration.