The optimal design of the batch chromatographic process for separation of valine (product) from isoleucine and leucine (side-products) was carried out by using the relevant optimization tool that was prepared on the basis of an up-to-date genetic algorithm. In such an optimal design, the flow rate, feed size (Δfeed), eluent gap size (Δgap), and product collection time were optimized to maximize the valine productivity of the batch chromatographic process under consideration. The results showed that the valine productivity was governed by the flow rate in the region of low flow rates, whereas it was governed by the Δgap/Δfeed factor in the region of high flow rates. Finally, the effect of valine yield on the productivity was investigated, followed by providing the proper operating conditions that could be advantageous to both valine productivity and valine yield.