Multiple system atrophy (MSA) is a rare disease with an extremely poor prognosis, for which no effective treatment currently exists. In recent years, non-invasive neuromodulation techniques have shown significant advantages in the field of neurodegenerative diseases. Transcranial magnetic stimulation (TMS), as a non-invasive neuromodulation technique, has demonstrated potential in the treatment of various neurological disorders. This article aims to review the latest research progress on TMS for MSA, with a particular focus on the evidence of its efficacy against core motor symptoms (such as parkinsonism and ataxia) and some non-motor symptoms in MSA patients. The feasibility of broadly implementing TMS in the clinical management of MSA is also discussed.