Brazil has experienced a Zika virus (ZIKV) outbreak with increased incidence of congenital malformations and neurological manifestations. We describe a case of a 26-year-old Brazilian Caucasian man infected with ZIKV and diagnosed with encephalomyelitis. Brain and spinal cord images showed hyperintense lesions on T2 and fluid-attenuated inversion recovery (FLAIR), and levels of proinflammatory cytokines in the cerebrospinal fluid showed a remarkable increase of interleukin (IL)-6 and IL-8. The observed pattern suggests immune activation during the acute phase, along with the neurological impairment, with normalization in the recovery phase. This is the first longitudinal report of ZIKV infection causing encephalomyelitis with documented immune activation.