BACKGROUND Infrared thermography is a diagnostic method used to monitor acute and chronic orofacial pain syndrome. Repetitive transcranial magnetic stimulation (rTMS) is a form of non-invasive brain stimulation. This prospective study from a single center aimed to investigate the effects of rTMS and used infrared thermography as a confirmatory test of orofacial pain. MATERIAL AND METHODS We used infrared thermography to examine the incidence of inflammatory changes as orofacial pain triggers. During the analysis of rTMS effects on patients with orofacial pain, we compared the decrease in pain and the thermal difference in the study group (n=17) and in the research group (n=13). RESULTS In the control group (n=13), there were no statistically significant changes. Both groups showed a significant decrease in self-reported pain. Numerical pain rating scores were significantly lower after S2 stimulation than after S1/M1 (P=0.0071) or sham (P=0.0187) stimulation. The Brief Pain Inventory scores were also lower 3 to 5 days after S2 stimulation than at the pretreatment baseline (P=0.0127 for the intensity of pain and p=0.0074 for the interference of pain), and after S1/M1 (P=0.001 and P=0.0001) and sham (P=0.0491 and P=0.0359) stimulations. CONCLUSIONS The findings from this study support the role of infrared thermography for the diagnosis of chronic orofacial pain, and showed that on the first and fifth days of rTMS therapy in the study group there was a significant reduction of the thermography findings when compared with the control group without rTMS therapy.