Background: Obesity is associated with changes in the nervous system, including a decrease in the speed of signal conduction and morphological changes in nerve cells. Therefore, the aim of this study was to investigate the effect of eight weeks of endurance training on the expression of neuregulin and agrin genes in obese rats. Materials and Methods: In this study, 20 male Wistar rats with a weight range of 349.44±41.68 grams were purchased. After making sure that they were familiar with the laboratory environment, the rats were divided into two groups. For eight weeks, the experimental groups performed five sessions of endurance training with an intensity of 70-80% of the maximum speed. Blood sampling was done 48 hours after the last training session and after 12 hours of fasting. Real Time-PCR method was used to measure the gene expression of neuregulin and agrin peptide. To check the normality of the data distribution, the Shapiro-Wilk test, the homogeneity of the data, the Levine test, the intra-group comparison of the dependent t and the inter-group comparison of the independent t were used. Hypotheses were tested with a significance level of P<0.05. Results: The statistical results showed that eight weeks of endurance training increased the expression of the neuregulin-1 gene (P=0.001) and decreased the expression of agrin peptide gene (P=0.001). Conclusion: It appears that eight weeks of endurance training resulted in amelioration of neurological conditions following obesity as well as led to positive changes in factors affecting nervous systems.