In this study, a single five-zone SMB system is applied for the complete separation of three amino acids mixture. Since only one SMB unit is used for the separation of the ternary mixture, the resulting capital and operational costs can have much savings, compared to other types of SMB configurations that are usually two SMB units in series. The zone flow rates and switching time of the five-zone SMB system in this study are determined from the equilibrium theory and then consider some margins to ensure high product purities for the three amino acids. Furthermore, the margin values are optimized for the maximization of a purity index, which is defined as the average of the three product purities. Finally, the throughput per bed volume of the developed SMB system is compared with those of other SMB configurations for the separation of the ternary mixture.