Ambient mass spectrometry (AMS) allows direct desorption and ionization of analytes in real time with minimal-to-no sample preparation. However, it may present inadequate capabilities for differentiating isomers. Here, a reactive flowing atmospheric-pressure afterglow (reactive-FAPA) AMS source is developed for rapid isomer differentiation by derivatization of analytes in real time. The effects of the reactive-FAPA operating conditions on the reagent and product ions were studied and optimized for highly volatile and non-volatile model compounds with different carbonyl functional groups. In addition, two functional isomers of valproic acid (VPA) metabolites, 4-ene VPA and γ-valprolactone, are successfully differentiated for the first time by incorporating methylamine (MA) reagent vapor into the plasma effluent used for desorption/ionization. Reactive-FAPAMS for 4-ene VPA shows only detectable peaks of the protonated acylation product [M + MA-H2O + H]+, while for γ-valprolactone, it shows detectable peaks for both protonated acylation product [M + MA-H2O + H]+ and protonated intermediate [M + MA + H]+. A method for quantitative characterization of mixtures of 4-ene VPA and γ-valprolactone is also developed and validated. In addition, reactive-FAPAMS also shows better detection sensitivity compared to nonreactive-FAPAMS for some larger analyte types, such as UV filters and steroids. The limit of detection (LOD) of pregnenolone acetate in reactive-FAPAMS is 310 ng/mL, which is about 10 times better than its LOD in nonreactive-FAPA.