The endothelial glycocalyx mediates interactions between the blood flow and the endothelium. This study aims to evaluate, quantitatively, effects of structural change of the glycocalyx on stress distribution and shear rate on endothelial cells. In the study, the endothelial glycocalyx is modeled as a surface layer of fiber matrix and when exposed to laminar shear flow, the matrix deforms. Fluid velocity and stress distribution inside the matrix and on cell membranes are studied based on a binary mixture theory. Parameters, such as the height and porosity of the matrix and the drag coefficient between fluid and matrix fibrils, are based on available data and estimation from experiments. Simple theoretical solutions are achieved for fluid velocity and stress distribution in the surface matrix. Degradation of the matrix, e.g., by enzyme digestion, is represented by reductions in the volume fraction of fibrils, height, and drag coefficient. From a force balance, total stress on endothelial surface remains constant regardless of structural alteration of the glycocalyx. However, the stress that is transmitted to endothelial cells by direct “pulling” of fiber branches of the glycocalyx is reduced significantly. Fluid shear rate at the cell membrane, on the other hand, increases. The study gives quantitative insight into the effect of the structural change of the glycocalyx on the shear rate and pulling stress on the endothelium. Results can be used to interpret experiments on effects of the glycocalyx in shear induced endothelial responses.