Abstract The enzymatic hydrolysis of microalgae has already been studied for bioethanol production. However, the enzymatic hydrolysis of microalgae under various fluid hydrodynamic conditions has not been simulated yet. Accordingly, the present study investigated the effect of various stirrer speed values, impeller types, and the presence of baffles on glucose extraction from the mixed microalgae using cellulase. The Michaelis-Menten kinetic constants of enzymatic hydrolysis were calculated in the AQUASIM and were used for simulation in COMSOL. The simulated values agreed with the experimental results and revealed that the low stirring speed reduced glucose extraction through undesirable enzyme distribution and the formation of regions with a high concentration of hydrolysis products to inhibit the enzyme's operation. The higher uniformity of glucose concentration at higher stirring speeds compared to lower stirring speeds ensured the higher efficiency of the mixing process in this reactor. The study findings suggested that a sufficient understanding of the mixing effects in the enzymatic hydrolysis could improve the economic feasibility of the process. Furthermore, compared to the unbaffled reactor, the proper mixing in the baffled reactor increased the enzymatic hydrolysis rate. It was found that altering the impeller type leads to a negligible change in the enzymatic hydrolysis rate.