Continuous or integrated downstream processing is expected to increase the productivity of protein drug production. However, it is not easy to design and operate continuous downstream processing as many batch chromatography unit operations are involved. An operation method known as flow-through chromatography (FTC) is an efficient method for separating a target protein. In FTC, a target protein is recovered from the chromatography column without adsorption whereas contaminants are tightly bound. Although the operation is simple, choosing the right mobile phase, column dimension and operating conditions is not easy as the separation is quite sensitive to mobile phase salt concentration and pH as well as operating conditions. In this study, we developed an optimization method for FTC. The model system was removal of protein dimer from the monomer by anion exchange chromatography. It was shown that by choosing the right mobile phase salt concentration and the flow-velocity (residence time) similar high productivities can be obtained at pH 6.0, 7.0 and 8.0.It was also found that FTC processes are quite sensitive to the mobile phase salt concentration.