Background: Cervical myelopathy (CM) is a common cause of morbidity and disability in patients with mucopolysaccharidosis (MPS) and, therefore, early detection is crucial for best surgical intervention and follow-up. Transcranial Magnetic Stimulation (TMS) non-invasively evaluates the conductivity along the cortico-spinal tract, also allowing preclinical diagnosis and monitoring. Methods: motor evoked potentials (MEPs) to TMS were recorded in a group of 8 patients with MPS-related CM. Responses were obtained during mild tonic contraction through a circular coil applied over the “hot spot” of the first dorsal interosseous and tibialis anterior muscles, bilaterally. Central motor conduction time was estimated as the difference between MEP cortical latency and the peripheral motor conduction time by cervical or lumbar magnetic stimulation. Peak-to-peak MEP amplitude to cortical stimulation and right-to-left difference of each parameter were also measured. Results: TMS revealed abnormal findings from both upper and lower limbs compatible with axonal damage and demyelination in 6 of them. Notably, a subclinical cervical spinal disease was detected before the occurrence of an overt CM in two patients, whereas TMS signs compatible with a CM of variable degree persisted despite surgery in all treated subjects. Conclusions: TMS screening should be performed in MPS patients, before and after surgery.