Propofol is a short-acting, intravenously administered hypnotic agent which is used in procedural sedation in children. Propofol is known to decrease systemic vascular resistance, arterial blood pressure and can lead to desaturations and decreased systemic perfusion in children with cardiac shunting. This may result in a reduction in cerebral blood flow and oxygenation. Near-infrared spectroscopy (NIRS) can monitor cerebral tissue oxygenation in the frontal neocortex. The objective of our study was to measure the changes in cerebral oxygen and blood supply after Propofol infusion in children with congenital heart disease. Propofol infusion may reduce cerebral oxygenation in children with congenital heart disease. The study group consisted of 32 children (f:m = 18:14), with median age of 49 (5–112) months and median weight of 15 (5–34) kg. We performed NIRS derived continuous measurement of cerebral oxygenation and cardiac output using Electrical velocimetry for 5 min before and after sedation with Propofol (1–2 mg/kg i.v.) for cardiac catheterization. Simultaneously, non-invasive arterial blood pressure and transcutaneous oxygen saturation were measured. Propofol sedation led to a significant decrease in mean arterial pressure (79 ± 16 vs. 67 ± 12 mmHg) (p = 0.01) and cardiac index (3.2 ± 0.8 vs. 2.9 ± 0.6 ml/min/m²) (p = 0.03). In contrast, cerebral tissue oxygenation index, increased significantly from 57 ± 11 to 59 ± 10 % (p < 0.05). Sedation with Propofol increased cerebral tissue oxygenation despite a decrease in cardiac index and arterial blood pressure. This may be caused by a decreased oxygen consumption of the sedated brain with intact cerebral auto-regulation.