Hyperthermal ion/surface collisions of bromotoluene radical cations were studied using perfluorinated (F-SAM) and hydroxyl-terminated (OH-SAM) self-assembled monolayer surfaces in a tandem mass spectrometer with BEEQ geometry. The isomers were differentiated by ion abundance ratios taken from surface-induced dissociation (SID). The dissociation rate followed the order of ortho > meta > para isomers. The peak abundance ratio of m/z 51 to m/z 65 showed the best result to discern the isomers. A dissociation channel leading to tolylium ion was suggested to be responsible for the pronounced isomeric differences. The capability of SID to provide high-energy activation with narrow internal energy distribution may have channeled the reaction into the specific dissociation pathway, also facilitating small differences in reaction rates to be effective in the spectral time window of this experiment. All of the molecular ions experiencing reactive collisions with the F-SAM surface undergo transhalogenation, in which a fluorine atom on the surface replaces the bromine in the incoming ions. This reactive collision was dependent on the laboratory collision energy occurring in ca. 40.75 eV range.