Background and Aim: Induction of experimental autoimmune encephalomyelitis (EAE) is associated with an overexpression of indoleamine 2,3-dioxygenase 1 (IDO1) and exacerbation of clinical symptoms. This study aimed to investigate the effect of physical activity on the gene expression of IDO1 and arylalkylamine N-acetyltransferase (AANAT) in the cerebellum of EAE mice. Materials and Methods: 30 C57BL/6 mice were randomly divided into three groups of 10: healthy control, EAE control, and physical activity in the enriched environment. Mice were placed in an enriched environment after induction of EAE with MOG35-55 for 4 weeks and then the cerebellum tissue was dissected and the gene expression of IDO1 and AANAT were measured by Real Time-PCR method in all three groups. Analysis of variance test was used for data analysis at a significance level of less than 0.05. Results: physical activity in an enriched environment compared to the EAE group significantly reduced the gene expression of IDO1 (P = 0.02), significantly decreased the gene expression of AANAT (P = 0.04) and also significantly reduced the clinical score (P = 0.001). Conclusion: Changing the environment and lifestyle in the enriched environment can prevent the progression of the MS autoimmune disease through downregulation of the gene expression IDO1 and AANAT.