Membrane filtration systems are preferred unit operations in industrial applications due to their mild operating conditions. However the performance of a membrane stack drops over time because of the membrane fouling. This decrease is overcomed by introducing clean membrane stacks. The associated scheduling problem, when to include new membrane stacks to the operation, is the main topic of this paper. We construct a dynamic optimization problem to find the optimal time instants of introducing new membrane stacks. Furthermore, the optimal operating pressure profile for the optimal scheduling strategy is constructed from the desired output specifications. The result of the simulation study indicates that the optimal scheduling strategy improves the operation by slowing down the accumulation of fouling.