Near-infrared (NIR) light has been shown to produce a range of physiological effects in humans, however, there is still no agreement on whether and how a single parameter, like the flicker frequency of NIR light, affects the brain. An 810 nm NIR LED was used as the stimulator. Fifty subjects participated in this experiment. Forty subjects were randomly divided into four groups. Each group underwent a 30-minute NIR LED radiation with four different frequencies (i.e., 0 Hz, 5 Hz, 10Hz and 20 Hz, respectively) on the forehead. The remaining 10 subjects formed the control group, in which they underwent a 30-minute rest period without light radiation. EEG signals of all subjects during each test were recorded. Gravity frequency (GF), relative energy change, and sample entropy were analyzed. The experimental groups had larger GF values compared to the control group. Higher stimulation frequency would cause larger growth of GF (F = 14.75, P < 0.001). The amplitude of alpha waves relative energy increased, while theta waves decreased remarkably in the experimental groups (p < 0.02), and the extent of increase/decrease was larger at higher stimulation frequency, compared to that of the control. Sample entropy of electrodes in the frontal areas were much larger than those in other brain areas in the experimental groups (p < 0.001). Larger frequency of the NIR LED light would cause more distinct brain activities in the stimulated areas. It indicates that NIR LEDlightmay have a positive effect onmodulating brain activity.These resultsmay help improve the design of photobiomodulation treatments in the future.