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 10 h of the hydrolysis performed under mixing conditions equaled 2.37 g and 2.39 g for the pressure of 0.4 and 0.6 bar, respectively. They correspond to the high hydrolysis yield, equaled in average to 99.1 %.