Hemodynamics including flow pattern, shear stress, and blood viscosity characteristics has been believed to affect the development and progression of arterial stenosis, but previous studies lack of realistic physiological considerations such as irregular surface geometry, non-Newtonian viscosity characteristics and flow pulsatility. The effects of surface irregularities and non-Newtonian viscosity on flow fields were explored in this study using the arterial stenosis models with 48% arterial occlusions under physiological flow condition. Computational flow dynamics based on the finite volume method was employed for Newtonian and non-Newtonian fluid. The wall shear stresses (WSS) in the irregular surface model were higher compared to those in the smooth surface models. Also, non-Newtonian viscosity characteristics increase the peak WSS significantly. The dimensionless pressure drop and the time averaged WSS in pulsatile flow were higher than those in steady flow. But pulsatility effects on pressure and WSS were less significant compared to non-Newtonian viscosity effects. Therefore, irregular surface geometry and non-Newtonian viscosity characteristics should be considered in predicting pressure drop and WSS in stenotic arteries.