The efficient separation of 5-hydroxymethylfurfural (HMF) – a platform chemical in the utilization of biomass – from the reactive aqueous sugar mixture is the key to improving its economic production. Here we show a cyclic fixed bed process that selectively adsorbs HMF from the aqueous phase, purifies the dissolved substance and enables its subsequent desorption in a suitable solvent for downstream applications. This intensified process bypasses the traditional energy-intensive recovery of HMF through vacuum distillation. The adsorption and desorption performances of a commercially available spherical polymer-based activated carbon (PBSAC) are quantified in discontinuous and continuous systems. The effects of temperature (25 – 90 ° C) and the coexistence of other components from the fructose dehydration reaction (fructose, formic acid and levulinic acid) on adsorption are assessed. Model predictions based on parameters extracted from batch isotherms reasonably describe the continuous experimental breakthrough curve with appropriate transport parameters. It is shown that HMF can be selectively purified and recovered and the adsorption column can be reused for at least seven cycles tested here. A simple analysis also shows almost ten times the cost and energy savings for HMF separation. The framework described here can be applied to other dissolved biomass.