- Our aim was to investigate, in a pilot study, the clinical and neurophysiological effects of non-invasive, deep repetitive transcranial magnetic stimulation (DrTMS) in Parkinson’s disease (PD), using the H coil. Twenty patients (3F; 63 ± 9 y.o.; PD duration: 6 ± 3 y) underwent 12 DrTMS sessions in 4 weeks. Excitatory 10 Hz DrTMS was applied over the primary motor cortex contralateral to the patient’s worse side (WS) and the bilateral prefrontal cortices. Motor control was assessed before and after DrTMS, OFF medication, using clinical (UPDRSIII, lateralized scores, timed arm tapping, and Nine-Hole Peg Test) and neurophysiological measurements (Event-Related Desynchronization (ERD) of the mu and beta sensorimotor rhythms during self-paced WS wrist extensions). No drop-outs or adverse events were recorded. UPDRSIII (global and subscores) and timed tests significantly improved after treatment (p < 0.001). Mu and beta ERD latency onsets were significantly increased after treatment (Mu: −1237 ± 177 ms before, and −2024 ± 215 ms after; beta: −1247 ± 151 ms before, and −2229 ± 179 ms after; p < 0.01). DrTMS is a safe treatment for PD. It improved motor symptoms and significantly modulated the cerebral activity related to motor planning. Further placebo controlled, randomized studies are needed to assess the therapeutic efficacy DrTMS and its consequences on cortical motor control.