Lock-In Amplifiers (LIA) represent a powerful technique helping to improve signals detectability when low signal to noise ratios are experienced. Continuous Wave functional Near Infrared Spectroscopy (CW-fNIRS) systems for e-health applications usually suffer of poor detection due to the presence of strong attenuations of the optical recovering path and therefore small signals are severely dipped in a high noise floor. In this work a digital LIA system, implemented on a Zynq® Field Programmable Gate Array (FPGA), has been designed and tested to verify the quality of the developed solution, when applied in fNIRS systems. Experimental results have shown the goodness of the proposed solutions.