Physical activity has profound effects on neuronal progenitor cell growth, differentiation, and integration, but the mechanism for these effects is still ambiguous. Using a mouse model, we investigated the effects of two weeks of treadmill running on the dynamics of the size distribution and miRNA profiles of serum extracellular derivatives (EDs) using particle-sizing analysis and small RNA sequencing. We found that an increased average diameter of EDs in the running group compared with the sedentary group (p < 0.05), and 16 miRNAs were significantly altered (p < 0.05) in the running group. Furthermore, functional annotation analysis of differentially expressed miRNA-predicted target genes showed that many of these target genes are involved in the PI3K-Akt pathway. Exercise-induced serum EDs increased Neuro2A cell viability and Akt phosphorylation. We also found that expression levels of neuronal maturation markers such as Microtubule-Associated Protein 2 (MAP2ab) and Neuronal nuclei (NeuN) were increased (p < 0.05, respectively), and that inhibition of the PI3K-Akt pathway by LY294002 pre-treatment ameliorated their expression in Neuro2A cells. Finally, the administration of exercise-induced EDs for 3 days increased the Histone 3 phosphorylation and β-III tubulin expression in Ink/Arf null neural stem cells and progenitors (NSPCs) under each proliferation and differentiation condition. These results suggest that exercise-induced circulating EDs may mediate neuronal maturation during exercise.