Design simulations of a simulated moving-bed (SMB) chromatography unit for the separation of fructooligosaccharides (FOS) were carried out. Using the constraints on the FOS purity in the raffinate of 90?% and FOS yield in the raffinate higher than 95?%, optimal distribution of a system of twelve columns into individual process zones and optimal values for the port switching period and the flow rates were found. The optimization function was the maximum productivity of FOS when the other evaluated performance criteria were the eluent consumption and product dilution. The performance of the designed SMB system was compared to that of a batch chromatography system that was simulated for a battery of identical columns. The sensitivity of the found optimum was analyzed with respect to the optimization parameters.