Experimental autoimmune encephalomyelitis (EAE) is a mouse model for the human multiple sclerosis, which is characterized by inflammation in the central nervous system (CNS), de-myelination of axonal neurons, and loss of motor coordination. The aim of the current study was to evaluate the effect of intranasal administration of mesenchymal stem cells (MSCs) and small extracellular vesicle (SEV) derived from the MSC (MSC-SEV) on disease activity and antigen-specific responses in the EAE mouse model. MSCs (5 × 105) were administered intranasally to EAE mice (n = 5) on the 15th and 24th days after immunization. In addition, the intranasal administration of MSC-SEV (10 μg) was used to treat EAE mice (n = 5) on a daily basis from the 15th to the 27th day after induction of the disease. The outcomes of therapies were evaluated using studying clinical symptoms and histological analysis of CNS lesions. Moreover, T cell proliferation, the frequency of regulatory T cells, the expression of transcription factors of T-helper subsets, and the levels of their corresponded cytokines were evaluated in splenocytes culture that was stimulated with specific-antigen. The results of treatment of EAE mice with MSC- SEV and MSC showed a significant decrease in the clinical scores, and it was found that treatment with MSC-SEV was more effective in alleviating clinical scores than MSC. In addition, the decrease in clinical symptoms was associated with an increase in immunomodulatory responses, including an increase in the frequency of Foxp3+ CD25+ regulatory T cells. Moreover, the level of TGF-β was increased by both treatments; however, interleukin-10 was increased only by MSC treatment. Ultimately, it was achieved that the intranasal administration of MSC-SEV to EAE mice was more effective than the administration of MSC to reduce clinical scores and histological lesions of the CNS tissue.