Background: Parkinson's disease (PD) presents a significant challenge due to its wide range of motor, non-motor, and treatment-related symptoms. Non-invasive interventions like transcranial magnetic stimulation (TMS) are being explored for potential therapeutic benefits. This study aimed to assess if a high-frequency repetitive TMS protocol (HF-rTMS) consisting of 10 trains of 100 pulses of rTMS at 25 Hz over the motor cortex (M1) at 80% of the resting motor threshold could be effective in treating motor or non-motor symptoms in patients with PD with levodopa-induced dyskinesias. Methods: A randomized, single-blinded, placebo-controlled pilot trial was conducted with eleven PD patients. Nine patients received HF-rTMS, while two received sham stimulation. Patients were exhaustively evaluated using validated clinical scales to assess motor and non-motor symptoms. The study followed a rigorous protocol to avoid bias, with assessments conducted by a neurologist specialized in single-blinded movement disorder. Results: The HF-rTMS group experienced a statistically significant slight worsening in both motor and non-motor symptoms, particularly in the mood/cognition and gastrointestinal domains. However, positive effects were observed in some non-motor symptoms, specifically reduced excessive sweating and weight. No adverse effects were reported. Conclusions: Although HF-rTMS did not produce significant motor improvements, its potential benefit on specific non-motor symptoms, such as autonomic regulation, warrants further investigation.