NIRS (Near-infrared spectroscopy) is a relatively, new, non-invasive, and non-ionizing method of measuring hemodynamic responses in thick biological tissues such as the cerebral cortex. In this study, we measured the hemodynamic responses of the rat barrel cortex to whisker stimulation by using a frequency-domain NIRS system. We designed multiple optical probes comprising multi-mode optical fibers and manipulating arms, both of which can be easily applied to small animals. Various electrical stimulations were applied to rat whiskers at different voltage levels and stimulation frequencies. Our results show that the hemodynamic responses are highly dependent on the stimulation voltage level, and not so much on stimulation frequency. This paper suggests that NIRS technology is highly suitable for the study of small animal brains.