We introduce a confocal functional near-infrared spectroscopy (fNIRS) imaging system that utilizes a time-gated photon-counting technology. This innovative approach enables the acquisition of high sensitivity and high spatial resolution information within a confocal array while considering cost-effectiveness. The performance of the system is confirmed through a series of functional tests and phantom experiments. Results from these tests show that the system can freely set the position and width of the time gating window within a range of 0 to 10 ns, with a temporal resolution of 10 ps. Phantom experiment results indicate that the system achieves a quantitative ratio improvement of over 32.9% in the confocal array, an enhancement of more than 31.6% in the contrast-to-noise ratio, and an increase of over 29.5% in spatial fidelity. Therefore, the confocal fNIRS imaging system designed in this study, using time-gated photon-counting technology, effectively improves imaging quality at a reasonable cost. This provides instrumental support and methodological reference for related fNIRS research.