We estimated cerebral oxygenation during handgrip exercise and a cognitive task using an algorithm that eliminates the influence of skin blood flow (SkBF) on the near-infrared spectroscopy (NIRS) signal. The algorithm involves a subtraction method to develop a correction factor for each subject. For twelve male volunteers (age 21 ± 1 yrs) +80 mmHg pressure was applied over the left temporal artery for 30 s by a custom-made headband cuff to calculate an individual correction factor. From the NIRS-determined ipsilateral cerebral oxyhemoglobin concentration (O2Hb) at two source-detector distances (15 and 30 mm) with the algorithm using the individual correction factor, we expressed cerebral oxygenation without influence from scalp and scull blood flow. Validity of the estimated cerebral oxygenation was verified during cerebral neural activation (handgrip exercise and cognitive task). With the use of both source-detector distances, handgrip exercise and a cognitive task increased O2Hb (P < 0.01) but O2Hb was reduced when SkBF became eliminated by pressure on the temporal artery for 5 s. However, when the estimation of cerebral oxygenation was based on the algorithm developed when pressure was applied to the temporal artery, estimated O2Hb was not affected by elimination of SkBF during handgrip exercise (P = 0.666) or the cognitive task (P = 0.105). These findings suggest that the algorithm with the individual correction factor allows for evaluation of changes in an accurate cerebral oxygenation without influence of extracranial blood flow by NIRS applied to the forehead.