Identifying small sugar isomers can be challenging by ion mobility-mass spectrometry (IM-MS) alone due to their small collision cross section differences. Herein, we report IM-MS results for multi-site, covalent carbohydrate derivatization with 3-carboxy-5-nitrophenylboronic acid (3C5NBA). Following reaction in aqueous solutions at room temperature, 3C5NBA reacts with each mono- or disaccharide molecule to yield products that each have a distinguishable mobility signature. The reaction was rapid and resulted in the detection of products within 5 min after 3C5NBA was mixed with the analyte. Eight disaccharides that varied in linkage, composition, and configuration (α or β) as well as four monosaccharides, d-glucose, d-galactose, d-mannose and d-fructose, were included in this study. The derivatives' drift times showed significant shifts, with up to 3-fold gains in resolution when compared to previous literature reports. Moreover, the specific MS/MS fragmentation information gathered from these sugar derivatives provided further validation of the isomers' structures.