Disarmament treaties have been the driving force towards reducing the large nuclear stockpile assembled during the Cold War. Further efforts are built around verification protocols capable of authenticating nuclear warheads while preventing the disclosure of confidential information. This type of problem falls under the scope of zero-knowledge protocols, which aim at multiple parties agreeing on a statement without conveying any information beyond the statement itself. A protocol capable of achieving all the authentication and security requirements is still not completely formulated. Here we propose a protocol that leverages the isotopic capabilities of NRF measurements and the classification abilities of neural networks. Two key elements guarantee the security of the protocol, the implementation of the template-based approach in the network’s architecture and the use of homomorphic inference. Our results demonstrate the potential of developing zero-knowledge protocols for the verification of nuclear warheads using Siamese networks on encrypted spectral data.