One of the remaining challenges in functional connectivity (FC) studies is investigation of the temporal variability of FC networks. Recent studies focusing on the dynamic FC mostly use functional magnetic resonance imaging as an imaging tool to investigate the temporal variability of FC. We attempted to quantify this variability via analyzing the functional near-infrared spectroscopy (fNIRS) signals, which were recorded from the prefrontal cortex (PFC) of 12 healthy subjects during a Stroop test. Mutual information was used as a metric to determine functional connectivity between PFC regions. Two-dimensional correlation based similarity measure was used as a method to analyze within-subject and intersubject consistency of FC maps and how they change in time. We found that within-subject consistency () is higher than intersubject consistency (). Within-subject consistency was not found to be task-specific. Results also revealed that there is a gradual change in FC patterns during a Stroop session for congruent and neutral conditions, where there is no such trend in the presence of an interference effect. In conclusion, we have demonstrated the between-subject, within-subject, and temporal variability of FC and the feasibility of using fNIRS for studying dynamic FC.