Background: There is evidence that both high and low frequency repetitive transcranial magnetic stimulation (rTMS) may have therapeutic effects on motor performance of Parkinson's disease (PD). Objective: The aim of the study was to conduct direct comparison of the two approaches. Patients and Methods: Sixty PD patients who attended The Neurology Clinic of Kobri El-Koba Military Hospital, Maadi Military Hospital and Al-Hussien University Hospital, Egypt from December 2018 to October 2019. They were randomly classified into three groups. Group I (sham group) received inactive stimulation, Group II received 5 Hz and group III received 1 Hz rTMS with a total of 2000 pulses over primary motor cortex (M1) of each hemisphere for ten days. Effects were assessed with the Unified Parkinson's Disease Rating Scale part III (UPDRS) the day before stimulation, one week after the last session, and one month later. Results: There was a significant improvement in all parts of UPDRS part III after 5 Hz rTMS (group II), and the effect persisted for one month after stimulation. As regard the Stage of disease, according to modified Hoehn and Yahr staging, there was an improvement in group II staging as nine patients improved to stage 2 where balance was regained and three patients in stage 5, as the severest stage, where patients were chair bound or bedridden improved partially to stage 4 and became able to walk unassisted with difficulty. Conclusion: 5 Hz rTMS over M1 is superior to 1 Hz rTMS for motor symptoms of PD, particularly in advanced stages showing motor complication.