Biometrics-based user authentication has several advantages over traditional password-based systems for standalone authentication applications. The fingerprint is evaluated as the most realistic alternative up to the present time in the perspectives of availability, accuracy and economy. However, serious problems may cause if fingerprint information stored for user authentication is used illegally by a different person since it cannot be changed freely as a password due to a limited number of fingers. Recently, research in fuzzy fingerprint vault system has been carried out actively to safely protect fingerprint information in a fingerprint authentication system. In this paper, we propose the FPGA-based fuzzy fingerprint vault system for real-time processing. Based on the experimental results, we confirmed that the proposed system takes 0.53 second with 36 real minutiae and 400 chaff minutiae.