Enterovirus 71 (EV71) infection can induce encephalitis. Overt immune responses is suspected to cause severe symptoms, so anti-inflammatory agents, corticosteroids have been recommended for treatment. However, one clinical study reported that treatment with glucocorticoids, dexamethasone (Dex) exacerbates disease severity. Here we investigated Dex treatment on EV71 infection using the murine model and found that both long-term (14-day) and short-term (4-day) Dex treatment starting from 1 or 3 days postinfection increased the mortality and disease severity of infected mice. Dex treatment starting from 4 or 8 days postinfection did not affect mouse mortality and disease severity. Early Dex treatment starting from 1 day postinfection caused atrophy and enhanced apoptosis in lymphoid organs to decrease the numbers of lymphocytes (CD4+ T cells, CD8+ T cells, and CD19+ B cells) and to increase viral loads in infected tissues of mice. Our results demonstrate that Dex treatment has no beneficial effect on EV71 infection.