Near-infrared spectroscopy (NIRS) is generally accepted as a functional brain imaging technology for brain activation study. With multichannel highly sensitive NIRS instruments, it has become possible to assess functional connectivity of different brain regions by NIRS. However, the feasibility needs to be validated in complex cognitive activities. In this study, we recorded the hemodynamic activity of the bilateral prefrontal cortex (PFC) during a color-word matching Stroop task. Wavelet transform coherence (WTC) analysis was applied to assess the functional connectivity of all homologous channel pairs within the left/right PFC. Both the behavioral and brain activation results showed significant Stroop effects. The results of WTC analysis revealed that, bilateral functional connectivity was significantly stronger during both the incongruent stimuli and neutral stimuli compared to that of the rest period. It also showed significant Stroop effect. Our findings demonstrate that, NIRS becomes a valuable tool to elucidate the functional connectivity of brain cortex in complex cognitive activities.