A MRI-guided navigation solution for repetitive transcranial magnetic stimulation (rTMS)was designed in this study which integrates optical positioning system to perform positioning and tracking of the magnetic stimulation coil in real-time. The system includes the following procedures: segmentation and 3D reconstruction of brain anatomy from T1-weighted (T1W) MRI, coil calibration and localization, spatial registration between the subject's head and the MRI data and 2D/3D navigation. The 2D/3D navigation provides the spatial relationship between actual sites of the coils and the cortical surface quantitively and allows visualization of the location and orientation of the coil over the brain/head. Verified through the experiments using a phantom human skull model and the head MRI data from a healthy human subject, the proposed navigation system was demonstrated to be flexible, safe, accurate and time efficient.