A 14-year-old standardbred mare with clinically suspected acute bronchitis was killed because of rapidly progressing central nervous disturbances. Necropsy revealed systemic granulomatous inflammation and vasculitis involving the lungs, thoracic lymph nodes, ribs, and liver. In the cerebrum there was a severe subacute bilateral encephalitis and malacia predominately affecting the white matter, and vasculitis with perivascular infiltration of lymphocytes, macrophages, and giant cells. A causative infectious agent could not be detected by Ziehl-Neelsen, Grocott, or Giemsa stains, by periodic acid–Schiff reaction of tissue sections, nor by bacterial and fungal cultures. Therefore, idiopathic systemic granulomatous disease (ISGD) was diagnosed and an immune-mediated pathogenesis was suspected. Inflammatory involvement of the brain has hitherto not been reported in cases of equine ISGD. This case seems to be an uncommon variant of ISGD with encephalitis and lack of dermal involvement.