We examined differences in brain activity in response to two types of mechanical stimulation, which have been reported previously as being perceptually indistinguishable but having different impacts on autonomic reflexes. As an indicator of brain activity, glucose metabolism was evaluated by PET with 2-[F]fluoro-2-deoxy-D-glucose (F-FDG). Twelve healthy, young adult men participated in the study. Two types of cutaneous stimulation tools, soft elastomer discs with microcones (microcone disc) or flat surfaces (flat disc), were used in a crossover, randomized double-blind manner. Each type of cutaneous stimulation tool was applied on the cheeks and F-FDG-PET scans were obtained. Greater F-FDG uptake was observed in the right anterior cingulate cortex during microcone disc stimulation compared with flat disc stimulation. However, F-FDG uptake during application of these two different stimuli was not different in the primary and secondary somatosensory cortices or insula. Stimulation using microcone discs and flat discs was noted by one and three participants, respectively, and there was no difference in the presence of perception between the stimulation tools. The results indicate that the right anterior cingulate cortex differentially responds to different types of cutaneous stimulation that are perceptually indistinguishable.