A 54-year-old male presented with a two-year history of recurrent syncope. Although he was treated with droxidopa and amezinium metilsulfate, his syncope was drug-resistant. Blood tests, cardiac evaluation and brain computed tomography (CT) were unremarkable. As his Schellong test was positive, orthostatic hypotension and syncope were the tentative diagnoses. Upon evaluating the patient neurologically while carefully avoiding syncope induction, mild cerebellar ataxia was observed. However, a brain magnetic resonance imaging (MRI) scan revealed a possible "cross sign" in the pons. Subsequent dopamine transporter single-photon emission computed tomography (DAT-SPECT) showed reduced uptake in the basal ganglia. Based on these findings, a clinical diagnosis of probable multiple system atrophy of the cerebellar type (MSA-C) was made, and treatment with taltirelin hydrate was initiated. This case underscores the importance of considering multiple system atrophy (MSA) in patients with persistent orthostatic hypotension and syncope, even before more obvious neurodegenerative symptoms emerge.