We derive limits on the intrinsic charm (IC) content of the proton, considering various theoretical models for IC and using as a basis the experimental upper limit on the prompt neutrino flux reported by the IceCube collaboration in their analysis of throughgoing muon tracks from the Northern Hemisphere. Our upper limit on the IC follows from the condition that the total prompt neutrino flux comprising the contributions from both the perturbative QCD heavy-flavour production and the process of freeing and hadronizing IC saturates the IceCube limit.