We describe a case of systemic lupus erythematosus (SLE) complicated with multifocal leukoencephalopathy (PML). A 57-year old woman, who had a five-year history of SLE, was admitted to our hospital because of fever and multiple subcutaneous nodules. Diagnosis of disseminated cryptococcosis was made based on histological and bacteriological examinations, and she was successfully treated with anti-fungal drugs. Corticoteroids were increased for persistent lupus activities. One month later, however, she gradually developed disorientation and short-term memory loss. A brain magnetic resonance image (MRI) showed a focal lesion in the white matter of the right frontal lobe. Brain biopsy demonstrated demyelinating lesions with the presence of JC viral antigen. Polymerase chain reaction also revealed JC virus DNA in the cerebrospinal fluid. Her condition gradually progressed, and she died a year later due to pneumonia. Although acquired immunodeficiency syndrome is currently the most common disease associated with PML, patients with autoimmune diseases receiving immunosuppressive therapy also have risks for developing PML. In patients with SLE presenting with subacute neurological abnormalities and white matter lesions in the brain, PML should be considered in the differential diagnosis.