The nondetection of neutrinos coming from Gamma Ray Bursts (GRBs) by the IceCube experiment has raised serious questions on our understanding of GRB’s and the mechanism of neutrino flux production in them. Motivated by this and the need for a precise calculation for GRB neutrino flux, here we study the effects of beyond standard model physics on the GRB neutrino flux. In the internal shock model of GRB, high energy neutrinos are expected from muon, pion and kaon decays. Using the latest best fit neutrino oscillation parameters, we compute the expected flux on earth for standard as well as non-standard oscillation scenarios. Among the non-standard scenarios, we consider neutrino decay, pseudo-dirac nature of neutrinos and presence of one eV scale light sterile neutrino. Incorporating other experimental bounds on these new physics scenarios, we show that neutrino decay scenario can significantly alter the neutrino flux on earth from the expected ones whereas the corresponding changes for pseudo-dirac and sterile neutrino cases are moderate. © 2013 Sociedade Brasileira de Fisica. All Rights Reserved.