The human neurotropic JC virus (JCV) is most commonly acquired during childhood, and, because no clinical illness has been associated with primary infection, is presumed to be asymptomatic. In the immunocompromised host, JCV is responsible for progressive multifocal leukoencephalopathy (PML). We describe a patient with longstanding systemic lupus erythematosus who presented with acute meningitis without encephalitis or PML. JCV was the only pathogen found in the cerebrospinal fluid suggesting a primary infection or symptomatic reactivation. Our observation demonstrates the expanding clinical importance of JCV in autoimmune diseases, and diagnostic tests for JCV should be included in the investigative work-up for meningitis or encephalitis in these patients.