In this work, a variational multiscale finite element formulation is used to study bifurcation flows of non-Newtonian fluids, using a representative simplified Carotid Artery geometry. In particular, the flow pattern and wall shear stress (WSS) computed using power-law, Cross, and Carreau–Yasuda models, are assessed. First, the formulation is validated by contrasting simulations of a benchmark test for bifurcation flows reported in the literature. After that, a study of blood flow through the carotid artery is presented. Hemodynamics conditions aimed to describe the flow behavior from diastole to systole of the cardiac cycle for healthy arteries and two specific conditions (60% carotid stenosis due to atherosclerosis and 20% increased bifurcation angle due to aging), are specifically analyzed. For each condition, the hemodynamics present different velocity fields that lead to distinctive distribution of WSS enable us to classified three regions, depending on their magnitude: low-WSS, medium-WSS and high-WSS. Results show that power-law flows predict lower wall shear stresses, especially in sections where geometry concentrates stresses, compared to those predicted using Cross and Carreau–Yasuda models. Overall, low-WSS are usually present in zones where stenosis develops even in healthy arteries, however, both geometries lead to a decrease of WSS magnitude in low-WSS regions, increasing the risk factor associated with plaque building.