Biometric authentication systems have become crucial for securing access to sensitive information and systems. Among various biometric traits, fingerprints are most widely used due to their uniqueness and permanence in multiple applications. These systems are susceptible to a range of threats, with one of the most significant being the security breach of biometric templates stored in the database. To mitigate these attacks, template protection mechanisms that utilize various cryptographic algorithms have been developed in the literature. However, the emergence of quantum computers threatens traditional cryptographic methods which consequently increases the demand for robust post-quantum cryptographic schemes to safeguard users’ stored data. In this work, we introduce a novel fingerprint template protection method utilizing the Hamming Quasi-Cyclic (HQC) technique, which is a post-quantum Key Encapsulation Mechanism (KEM) integrated with Advanced Encryption Standard (AES). HQC offers smaller key sizes and faster decryption times, making it highly suitable for environments with limited computational resources, as required in fingerprint authentication systems. The experiments were performed on the publicly available benchmark Fingerprint Verification Competition (FVC) 2004 dataset. The results indicate that our proposed template protection scheme outperforms existing state-of-the-art approaches in terms of time, size, and entropy-based evaluations. These findings demonstrate that the introduced template protection method enhances security against potential quantum attacks while providing a faster authentication system with reduced computational overhead.