Large Eddy Simulation (LES) is performed to study the physiological pulsatile transition-to-turbulent non-Newtonian blood flow through a 3D model of arterial stenosis by using five different blood viscosity models: (i) Power-law, (ii) Carreau, (iii) Quemada, (iv) Cross and (v) modified-Casson. The computational domain has been chosen is a simple channel with a biological type stenosis formed eccentrically on the top wall. The physiological pulsation is generated at the inlet of the model using the first four harmonic series of the physiological pressure pulse (Loudon and Tordesillas [1]). The effects of the various viscosity models are investigated in terms of the global maximum shear rate, post-stenotic re-circulation zone, mean shear stress, mean pressure, and turbulent kinetic energy. We find that the non-Newtonian viscosity models enlarge the length of the post-stenotic re-circulation region by moving the reattachment point of the shear layer separating from the upper wall further downstream. But the turbulent kinetic energy at the immediate post-lip of the stenosis drops due to the effects of the non-Newtonian viscosity. The importance of using LES in modelling the non-Newtonian physiological pulsatile blood flow is also assessed for the different viscosity models in terms of the results of the dynamic subgrid-scale (SGS) stress Smagorinsky model constant, C(s), and the corresponding SGS normalised viscosity.