Abstract: Light neutralinos could be copiously produced from the decays of mesons generated in cosmic-ray air showers. These neutralinos can be long-lived particles in the context of R-parity violating (RPV) supersymmetric models, implying that they could be capable of reaching the surface of the earth and decay within the instrumental volume of large neutrino detectors. In this article, we use atmospheric neutrino data from the Super-Kamiokande experiment to derive novel constraints for the RPV couplings involved in the production of long-lived light neutralinos from the decays of charged D-mesons and kaons. Our results highlight the potential of neutrino detectors to search for long-lived particles, by demonstrating that it is possible to explore regions of parameter space that are not yet constrained by any fixed-target nor collider experiments.