Adequate perfusion of blood is fundamental to brain tissue viability, and failure to appropriately regulate cerebral blood flow is related to neurological damage. Cerebral tissue oxygenation is commonly used as a surrogate of cerebral blood flow for non-invasive measures of autoregulation, but may only be valid during periods of constant oxygen delivery. We present a new algorithm to correct for supply oxygen-induced variations in cerebral tissue oxygenation, and we validate it by measuring the improved correlation of the corrected tissue oxygenation with blood flow. The algorithm corrects tissue oxygenation by calculating its linear dependence with arterial oxygen saturation below a baseline level. A porcine model (N=8) of hypoxia is used to test the algorithm and compare the tissue oxygen correction with a blood flow reference signal. The correction provides significant improvement in the correlation between flow and tissue oxygenation (Wilcoxon signed rank, p<;0.01), and for the root mean square distance between the corrected hypoxic periods and the rSO2-flow regression line (Wilcoxon signed rank, p<;0.01). This method allows the correction of tissue oxygenation levels used in the non-invasive monitoring of autoregulation.