The separation of an aqueous mixture of glucose and fructose was experimentally performed by using a semi-continuous chromatographic refiner (SCCR) which consists of purge, pre-feed section. Packing materials were Ca²⁺ ion form of DOWEX 50W 12X resin and water was used as an isocratic eluent. The plug flow model with velocity dependent mass transfer resistance was presented for calculating both products and on-concentrations in the SCCR unit. The effects of factors-the ratio of adsorbed phase to mobile phase flow rate, α(margin), purge rate and total number of columns in the SCCR operation-were studied and the validity of the model was experimentally confirmed. The modified SCCR operation without a purge section was also studied.