Blood flow behaves differently at the microvascular level than they do at upper levels of circulating systems. The endothelial glycocalyx layer on the luminal surface of blood vessels plays a significant role in regulating blood flow and blood cell movement in microvascular networks. For instance, previous experimental studies showed that the endothelial glycocalyx layer causes additional resistance to blood flow in small blood vessels. One of the important facts of the endothelial glycocalyx layer is that this layer is highly negatively charged. The question remains: do these electrostatic charges retard blood flow in small blood vessels according to the electroviscous effect? Here, a theoretical model is proposed to investigate the electrochemical effects of the endothelial glycocalyx layer on two-phase non-Newtonian blood flow in small blood vessels. Results show that electrostatic charges on the endothelial glycocalyx layer induce negligible effect to blood flow. Therefore, we can attribute the cause of additional resistance by the endothelial glycocalyx layer mainly to other mechanisms, such as, the glycocalyx constituted proteins acting as a flow barrier.