A 77-year-old woman presented with a 6-month history of slowly progressive cerebellar ataxia. T2-weighted MRI showed high signal intensity in the left upper dorsal pons and bilateral middle cerebellar peduncles. JC virus (JCV) DNA was detected in cerebrospinal fluid (CSF). The patient had no HIV infection, collagen disease, or a history of immunosuppressive treatment, but she was found to have CD4+ lymphocytopenia. We made a diagnosis of cerebellar brainstem form of progressive multifocal leukoencephalopathy (PML) presenting as cerebellar ataxia, which was presumably associated with idiopathic CD4+ lymphocytopenia. Following the treatment with mefloquine, the patient slightly improved clinically and JCV-DNA became negative in CSF.