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Functional near-infrared spectroscopy (fNIRS) has been increasingly utilized for detecting human cerebral activity in many disciplines because of the potential for less-restraining conditions. However, users often suffer from motion artifacts originating from optode fluctuation during task execution when the task includes motion. In such cases, the optode fluctuation induces changes both in the reflection by hair and in the transmission between the optode and scalp. If part of the reflected light is directly received by the detector optode (short-circuited light), it will contaminate the fNIRS signal. The transmittance change at the optode–scalp gap will also contaminate the signal. In this study, we proposed an optical model on the influence of optode fluctuation on the fNIRS signal and a method for removing the influence. The model revealed the following: (1) the received short-circuited light and the gap transmittance change generated a baseline change in the detected light intensity, and (2) the signal from the tissues was downscaled with increases in the receiving intensity of short-circuited light. To avoid erroneous detection of short-circuited light, we developed a method that optically eliminated hair-reflected light from the detection using linearly polarized light sources and an orthogonally polarized analyzer. The method was validated with an optical phantom possessing a haired surface. The optical absorbance change of a close source–detector (S-D) pair equipped with polarizers was very similar to that of distant S-D pairs, even though these optodes were artificially fluctuated. By combining the multidistance optode arrangement technique with the short-circuited light elimination method, the measurement could effectively eliminate motion artifacts originating from optode fluctuation.