Signal processing of brain activity poses challenges to various researchers from different areas, including medical, biomedical, and engineering researchers. Near-infrared spectroscopy (NIRS), as signal detecting and processing, has been used in medical imaging to obtain oxygenation and hemodynamic response in the cerebral cortex. As one of updated techniques, it has been evidenced useful, efficient, and effective in the medical examinations. It applied in cortical activation detection and functional connectivity in brain research. Despite some advances in functional lateralization, most of the studies have focused on the prefrontal cortex but little has been done to study the somatosensory region (S1). For this reason, the aim of our current study is to assess bilateral connectivity in the somatosensory region by using NIRS and noxious stimulation. A few healthy subjects were investigated using near-infrared spectroscopy during an acupuncture stimulation procedure to safely induce pain in subjects. A multiscale analysis based on wavelet transform coherence (WTC) was designed to assess the functional connectivity of corresponding channel pairs within the left and right S1 region. The distributions of the reactions based on WTC in the brain after the stimulations are presented by both time region and frequencies domain. The coherence in time-frequency domain between homologous signals generated by contralateral channel pairs increased during stimulation tasks but not during resting time. This study will contribute to the research field to investigate cerebral hemodynamic response of pain perception using NIRS.