We used magnetoencephalography (MEG) to investigate the cortical processing of an innocuous facial tactile stimulus in healthy subjects and in a group of subjects suffering from chronic temporomandibular disorder (TMD). Equivalent current dipoles (ECDs) were extracted for a time period of 1 s following stimulus application, and their location, duration and onset time determined. The counts of ECDs extracted did not differ significantly between the two groups. In contrast, we found statistically significant differences in ECD duration and onset time. Specifically, ECD duration was longer in the TMD group in the precentral gyrus, and ECD onset time was earlier in the parietal operculum. In addition, we found differences in the internal organization and clustering of the brain areas involved indicating a less tight association and a less coordinated stimulus information processing in the TMD group. Altogether, these results show that an innocuous facial tactile stimulus is differently processed in the brain of TMD subjects, when compared to controls, reflecting altered brain mechanisms due to chronic pain.