Central nervous system (CNS) infection by Theiler's murine encephalomyelitis virus (TMEV) causes an immune‐mediated demyelinating disease similar to human multiple sclerosis in susceptible mice. To understand the pathogenic mechanisms, we analyzed the level, specificity, and function of CD4+ Th cells in susceptible SJL/J and resistant C57BL/6 mice. Compared to resistant mice, susceptible mice have three‐ to fourfold higher levels of overall CNS‐infiltrating CD4+ T cells during acute infection. CD4+ T cells in the CNS of both strains display various activation markers and produce high levels of IFN‐γ upon stimulation with anti‐CD3 antibody. However, susceptible mice display significantly fewer (tenfold) IFN‐γ‐producing Th1 cells specific for viral capsid epitopes as compared to resistant mice. Furthermore, preimmunization with capsid‐epitope peptides significantly increased capsid‐specific CD4+ T cells in the CNS during the early stages of viral infection and delayed the development of demyelinating disease in SJL/J mice. This suggests a protective role of capsid‐reactive Th cells during early viral infection. Therefore, a low level of the protective Th1 response to viral capsid proteins, in conjunction with Th1 responses to unknown epitopes may delay viral clearance in susceptible mice leading to pathogenesis of demyelination during acute infection, as compared to resistant mice.