Functional near-infrared spectroscopy (fNIRS) is an effective tool to non-invasively investigate cerebral oxygenation and hemodynamics. fNIRS as well as other functional neuroimaging techniques including functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) have been used for investigating the neural mechanisms of functional recovery after a stroke or a traumatic brain injury. fNIRS has several advantages over other neuroimaging techniques in terms of clinical application in the field of rehabilitation medicine. In addition to its portability and low equipment cost, fNIRS does not require strict motion restriction during measurement, unlike other functional imaging techniques. Therefore, this technique enables the examination of cortical activation during physically dynamic activities, like gait or balance perturbation. Studies using fNIRS have revealed several implications for gait recovery after stroke. These studies have shown that the medial sensorimotor cortex (SMC) and the supplementary motor area (SMA) are mainly involved in steadying gait and that the prefrontal cortex (PFC) is involved in the adjustment of walking speed. In hemiparetic patients, lateralization of SMC activation during gait is reduced, and additional cortical activations in the premotor cortex and PFC during gait became evident after focused rehabilitation for several months. The cortical activation pattern may be modified after different types of rehabilitative interventions. These results imply that fNIRS data is a potential biomarker for functional recovery and the response to rehabilitative interventions. Although further studies are required, fNIRS might provide useful information for customizing rehabilitation programs in order to enhance functional recovery.