In this paper, we monitored the accuracy of nonnavigated application of repetitive Transcranial Magnetic Stimulation (rTMS) in 10 patients suffering from orofacial pain by using functional magnetic resonance (fMRI), computer modeling and numerical simulation. Through a unique process, each fMRI scan was used to define a Region of Interest (ROI) where the source of the orofacial pain was located, which was to be stimulated using rTMS. For each patient, MRI scans with a spatial resolution of 0.7 mm were converted into an anatomically accurate head model. The head model including the ROI was then co-registered with a model of the stimulation coil in an electromagnetic field numerical simulator. The accuracy of rTMS application was evaluated based on the calculations of electric field intensity distribution in the ROI. The research has yielded unique insight into ROIs (with average volume 904 mm 3 ) in patients with orofacial pain and has also extended further possibilities of human head MRI image semi-automatic segmentation. According to the calculations performed, the average ROI volume that was stimulated by an electric field with an intensity of over 80 V/m was only 4.4%, with the maximum ROI volume being 20.5%.Furthermore, a numerical study of the impact of coil rotation and translation was performed. It demonstrated a) the optimal placement of the stimulation coil can significantly increase the volume of the stimulated ROI up to 60% and b) patients with orofacial pain would need precise coil positioning with a navigation error lower than 10 mm. Due to an acceptable proccessing time of up to 6 hours, described numerical simulation opens up new options for precise rTMS treatment planning. This planning platform together withpatient-specific navigated rTMS, could lead to significant increase of treatment outcomes in patients suffering from orofacial pain.