This paper provides preliminary research regarding the implementation and evaluation of a hybrid mechanism of authentication based on fingerprint recognition interconnected with RFID technology, using Arduino modules, that can be deployed in different scenarios, including secret classified networks. To improve security, increase efficiency, and enhance convenience in the process of authentication, we perform a comparative assessment between two homomorphic encryption algorithms, the Paillier partial homomorphic algorithm and the Brakerski–Gentry–Vaikuntanathan fully homomorphic encryption scheme, applied to biometric templates extracted from the device mentioned above, by analyzing factors such as a histogram analysis, mean squared error (MSE), peak signal-to-noise ratio (PSNR), the structural similarity index measure (SSIM), the number of pixel change rate (NPCR), the unified average changing intensity (UACI), the correlation coefficient, and average encryption time and dimension. From security and privacy perspectives, the present findings suggest that the designed mechanism represents a reliable and low-cost authentication alternative that can facilitate secure access to computer systems and networks and minimize the risk of unauthorized access.