Non-ideal mixing is an important challenge in industrial scale enzymatic hydrolysis reactors. This work, therefore, optimizes a hydrolysis reactor after considering non-ideal mixing. The flow rate of heating fluid was used as the decision variable for maximization of glucose problem, and flow rate of the heating fluid and enzyme loading was used as decision variables for maximization of profit problem. The non-ideal mixing was represented by dividing the reactor into three levels and each level comprising 12 compartments connected to each other by circulation and exchange flows. Multiple cases with the substrate either uniformly or non-uniformly distributed in the reactor were studied. It was observed that the optimal decision variables for maximization of glucose problem were dependent on the substrate distribution for the initial hours of hydrolysis and the optimal decisions do not differ much in the later stages of hydrolysis. For maximization of profit problem, the enzyme requirement changed significantly, but the flow rate of heating fluid did not change much for the ideally mixed reactor. However, for the non-ideally mixed reactor, both the flow rate of the heating fluid as well as the enzyme requirement changed significantly. The use of optimal decisions from a non-ideally mixed reactor instead of an ideally mixed one lead to 3.19 % and 6.63 % reduction in deviation of glucose and profit from ideally mixed reactor.