Nuclear disarmament treaties are not sufficient in and of themselves to neutralize the existential threat of the nuclear weapons. Technologies are necessary for verifying the authenticity of the nuclear warheads undergoing dismantlement before counting them toward a treaty partner’s obligation. Here we present a concept that leverages isotope-specific nuclear resonance phenomena to authenticate a warhead’s fissile components by comparing them to a previously authenticated template. All information is encrypted in the physical domain in a manner that amounts to a physical zero-knowledge proof system. Using Monte Carlo simulations, the system is shown to reveal no isotopic or geometric information about the weapon, while readily detecting hoaxing attempts. This nuclear technique can dramatically increase the reach and trustworthiness of future nuclear disarmament treaties.