Repetitive transcranial magnetic stimulation (rTMS) has recently been assessed as a non-invasive treatment modality for neuropsychiatric disorders. However, the mechanisms underlying the therapeutic effects are still not understood. Studies in rodents revealed lasting effects in limbic-related regions, but species difference in brain structures makes it difficult to infer the regional effect in primate brain. To reveal how rTMS affects primate brain function, we performed positron emission tomography (PET) using 18F-fluorodeoxyglucose (FDG) and 11C-raclopride (RAC) in anaesthetized macaque monkeys. A total of 2000 pulses of 5Hz-rTMS were delivered on the unilateral primary motor cortex using a small coil. Voxel-based analysis revealed statistically robust changes in FDG activity in the motor, cingulate, and orbitofrontal cortices, as well as in binding potential of RAC in the ventral striatum. Interestingly, the change in FDG activity persisted at least 8 days. These results demonstrate that motor cortical rTMS induces dynamic functional changes in motor and limbic associated structures, suggesting its therapeutic effect on dysfunction of motor and motivation system.