Background: Non-invasive magnetic stimulation therapies have become a widespread neuromodulation method utilized in the treatment of mood disorders. Although these methods have shown efficacy in the treatment of psychiatric disorders such as bipolar affective disorder and depression, a few studies have been done on Parkinson's disease (PD). Objective: This study was executed to demonstrate the effectiveness of focused transcranial magnetic stimulation (fTMS) for the treatment of PD. For this aim, a new stimulation coil design with the semi-hexagonal core was used to concentrate magnetic flux in the particular innervation nucleus. Several TMS protocols were tested to stimulate the STN region of 6-OHDA lesioned rats to determine the most effective treatment. Results: The progress of treatment was investigated by recording and analyzing the neurophysiological activity of the primary motor cortex and locomotor behaviors. After 6-OHDA injection, sharp increases in the energy and power spectral density of beta and low- gamma band were caused. Also, the motor activities of rats reduced, and the degree of catalepsy increased significantly. By completing the proposed 1Hz r-TMS treatment, the amount of energy and power density in these bands diminished and came close to the baseline. Furthermore, debilitating motor fluctuations were reverted considerably. Conclusion: Experimental results reveal that after 40 days of the non-invasive procedure, both oscillatory activity and the locomotor behavior produce remarkable changes. The 1Hz r-TMS showed acceptable performance in a reduction of symptoms in the PD. The outcomes of the animal trials have raised some hopes to employ the findings of this study in human clinical research.