Natural deep eutectic solvents (NADESs) have been shown to be selective and environmentally friendly solvents for the extraction of bioactive compounds. However, studies on the solubility of low-molecular-weight carbohydrates (LMWCs) in NADESs are scarce. In this work, new solubility data of LMWCs in NADESs are provided and a new approach based on the use of these solvents for the efficient fractionation of bioactive carbohydrates was explored for the first time. Several mono- and disaccharides and three NADESs based on choline chloride (ChCl) and different donors (2-ethylene glycol (EtG), glycerol (Gly) and ethanedioic acid dihydrate (Eth)) were considered. While the degradation of carbohydrates, mainly ketoses, was detected with ChCl:Eth due to its acidic nature, ChCl:EtG and ChCl:Gly were found to be useful alternatives for selectively separating bioactive ketoses and their corresponding aldoses (e.g., lactulose/lactose and tagatose/galactose) present in equimolar binary mixtures. In addition, the usefulness of ChCl:EtG for the selective enrichment of lactulose to be used as food ingredient or nutraceutical was proven (from a 25% in the reaction mixture to a 56% in the purified sample). NADESs could be used for the selective fractionation of value-added carbohydrates from interfering sugars for several applications, including food science, engineering or pharmaceuticals.