The study of hemodynamics is particularly important in medicine and biomedical engineering as it is crucial for the design of new implantable devices and for understanding the mechanism of various diseases related to blood flow. In this study, we experimentally identify the cell free layer (CFL) width, which is the result of the Fahraeus–Lindqvist effect, as well as the axial velocity distribution of blood flow in microvessels. The CFL extent was determined using microscopic photography, while the blood velocity was measured by micro-particle image velocimetry (μ-PIV). Based on the experimental results, we formulated a correlation for the prediction of the CFL width in small caliber (D < 300 μm) vessels as a function of a modified Reynolds number (Re∞) and the hematocrit (Hct). This correlation along with the lateral distribution of blood viscosity were used as input to a “two-regions” computational model. The reliability of the code was checked by comparing the experimentally obtained axial velocity profiles with those calculated by the computational fluid dynamics (CFD) simulations. We propose a methodology for calculating the friction loses during blood flow in μ-vessels, where the Fahraeus–Lindqvist effect plays a prominent role, and show that the pressure drop may be overestimated by 80% to 150% if the CFL is neglected.