Background: Transcranial magnetic stimulation (TMS) can non-invasively probe cortical excitability in movement disorders, although clinical significance is still controversial, especially at early stages. We compare single-pulse TMS in two prototypic synucleinopathy and tauopathy—i.e., Parkinson’s disease (PD) and Progressive Supranuclear Palsy (PSP), respectively—to find neurophysiological differences and identify early measures associated with cognitive impairment. Methods: 28 PD and 23 PSP de novo patients were age-matched with 28 healthy controls, all right-handed and drug-free. Amplitude and latency of motor evoked potentials (MEP), central motor conduction time, resting motor threshold (rMT), and cortical silent period (CSP) were recorded through a figure-of-eight coil from the First Dorsal Interosseous muscle (FDI), bilaterally. Results: Mini Mental Examination and Frontal Assessment Battery (FAB) scored worse in PSP; PD had worse FAB than controls. Higher MEP amplitude from right FDI in PD and PSP than controls was found, without difference between them. CSP was bilaterally longer in patients than controls, but similar between patient groups. A positive correlation between FAB and rMT was observed in PSP, bilaterally. Conclusions: Despite the small sample size, PD and PSP might share, at early stage, a similar global electrocortical asset. rMT might detect and possibly predict cognitive deterioration in PSP.