Abstract: Heavy neutral leptons are predicted in many extensions of the Standard Model with massive neutrinos. If kinematically accessible, they can be copiously produced from kaon and pion decays in atmospheric showers, and subsequently decay inside large neutrino detectors. We perform a search for these long-lived particles using Super-Kamiokande multi-GeV neutrino data and derive stringent limits on the mixing with electron, muon and tau neutrinos as a function of the long-lived particle mass. We also present the limits on the branching ratio versus lifetime plane, which are helpful in determining the constraints in non-minimal models where the heavy neutral leptons have new interactions with the Standard Model.