Enzymatic hydrolysis is a crucial step in processing lignocellulosic biomass into biofuels and other valuable products in biorefineries. Applying a membrane reactor to realize this process allows for continuous separation of inhibitory end-products, thus improving process efficiency. Developed so far models have generally been dedicated to describing the reaction kinetics without considering transport phenomena and flux decline prediction. In the present paper, a new mathematical model simulating the hydrolysis process course in membrane bioreactor was established. Compared to previous reports, our study presents a novel approach to modeling the process accounting for the reaction course and permeate flux decline depending on reaction hydrodynamics. A surface renewal theory and empirical reaction kinetic model were implemented to simulate the influences of the operating parameters on the permeate flux and the monosaccharide concentration in the permeate. A procedure to determine the model parameters with experimental data was also presented. The proposed model simulated experimental data with good accuracy (R2>0.97). The total mass of glucose and xylose produced during 10h of the hydrolysis performed under mixing conditions equaled 2.37g and 2.39g for the pressure of 0.4 and 0.6bar, respectively. They correspond to the high hydrolysis yield, equaled in average to 99.1%.