Extensions of the Standard Model with charged Higgs, having a non-negligible coupling with neutrinos, can have interesting implications vis-à-vis neutrino experiments. Such models can leave their footprints not only in the ultra-high energy neutrino detectors like IceCube but can also give rise to the neutrino non-standard interactions (NSIs). We consider a model based on the neutrinophilic two-Higgs doublets and study its imprints in the excess neutrino events in the 1–3 PeV energy bins at the IceCube. This is facilitated by the existence of a charged scalar in the model which can result in a Glashow-like resonance. The same charged scalar can be responsible for sizeable NSIs. We perform a combined study of the latest IceCube data along with various other constraints arising from different neutrino experiments together with the limits set by the LEP experiment, and explore the parameter space which can lead to a sizeable NSI.