A five-zone simulated moving bed (SMB) process was developed in this study to recover sugars from corn-stover hydrolyzate. The sugars can serve as fermentation feedstock for ethanol production. The major hydrolyzate components are six sugars farabinose, mannose, xylose, galactose, glucose, cellobiose) and four impurities (sulfuric acid, acetic acid, furfural and hydroxymethyl furfural). An eight-zone SMB based on Dowex99 and a five-zone nonisocratic SMB based on poly-4-vinyl pyridine (PVP) were designed with pseudolinear standing wave design and then optimized. Cost analysis and fermentation tests indicated that the PVP SMB is the most cost-effective. The design was tested using VErsatile Reaction and SEparation (VERSE) simulations and SMB experiments. Two different feed compositions, two different feed flow rates, and two different regenerants were tested in three PVP SMB experimental runs. All runs had 99+% yields. The sugars purities ranged from 93% to 95%, because some sulfate and acetate co-eluted with the sugars. Discounting the salts results in purities of >99%. This study shows the model-based-design approach can achieve high yield and high purity for multicomponent separation in a five-zone nonisocratic SMB.