Development of acute experimental autoimmune encephalomyelitis (EAE) depends on Th17 cells expressing the nuclear factor NR4A2, which we have previously reported to be upregulated in peripheral blood T cells from patients of multiple sclerosis (MS). EAE induced in mice lacking NR4A2 in T cells showed a great reduction in Th17-mediated acute symptoms, whereas a late-onset disease independent of NR4A2 was still inducible. We identified cytotoxic T-cell-like CD4+ T cells expressing the T-box transcription factor Eomesodermin (Eomes) as a pathogenic component for the development of the late-onset disease. Furthermore, T cell-specific deletion of the Eomes gene or Eomes-specific RNA interference in vivo remarkably ameliorated the late-onset EAE. Intriguingly, similar Eomes-expressing CD4+ T cells are increased in the peripheral blood and cerebrospinal fluid only from patients with secondary-progressive MS accompanied by neurodegenerative symptoms, but not in relapsing-remitting MS. Mechanistic analysis revealed that granzyme B was secreted by Eomes-expressing CD4+ T cells and the activation of protease-activated receptor-1 by granzyme B is involved in the neuroinflammation observed in the late-onset EAE.