To investigate the therapeutic effect of navigator-guided repetitive transcranial magnetic stimulation (rTMS) for patients with atypical facial pain (AFP) after trigeminal nerve surgery, two patients with postoperative atypical facial pain were treated with 10 Hz rTMS on the primary motor cortex at 110% of the resting motor threshold (RMT) under the navigation, in 10 daily sessions, continuous stimulus 10 s per minute, intermittent 50 s, receiving 2500 pulses/day. Clinical assessment of the pain is performed with the Barrow Rating scale. After ten times of rTMS treatment, case 1 eased the pain from the barrow rating level V to level II, relief pain within 15 days after treatment, up to level III. Case 2 eased the pain from the barrow rating level IV to level I, relief pain within 2 days after treatment, up to level III. We conclude that the application of 10 Hz Navigator-guided rTMS on the primary motor cortex could significantly relieve AFP after trigeminal nerve surgery.