An efficient method for the extraction of hemodynamic responses in Near-Infrared Spectroscopy (NIRS) systems is proposed to increase the spatial and temporal resolution without hardware overhead. The performance improvement is attributed to high Signal-to-Noise-Ratio (SNR) receivers, a modulation scheme, and a Multi-Input-Multi-Output (MIMO) based data extraction algorithm. The proposed system shows an over 2× increment in the figure of merit (FOM) compared to conventional designs. Experimental results support the validity of the proposed system.