Musculoskeletal disorders including fracture, tendonitis, osteoarthritis, and laminitis are common diseases in racehorses that can cause large economic losses in the racehorse industry. Mesenchymal stem cells (MSCs) are being applied as new clinical tools for treatment of musculoskeletal disorders of racehorses. To investigate the immunomodulatory effects of stem cell therapy, we analyzed the anti- and pro-inflammatory factors in peripheral blood mononuclear cells of racehorses before and after stem cell application using quantitative real-time RT-PCR. The expression levels of pro-inflammatory factors (CCL5, IFN-γ, IL-2, and IL-18) were decreased while those of anti-inflammatory factors (TIMP-1, IL-10, TGF-β1, and VEGF) were increased significantly after application of equine adipose tissue-derived MSCs (eAD-MSCs) to racehorses with fracture. Moreover, the expression levels of pro-inflammatory factors (IL-2, IL-18, and TNF-α) were decreased while those of anti-inflammatory factors (TIMP-1, TIMP-2, IL-10, TGF-β1, and VEGF) increased significantly after stem cell application of eAD-MSCs in racehorses with tendonitis. After evaluating immunomodulatory effects of stem cell therapy on equine musculoskeletal disorders such as fracture and tendonitis, our results showed that expression levels of pro-inflammatory factors were decreased, while those of anti-inflammatory factors increased significantly after stem cell application of eAD-MSCs. These findings suggest that the healing effects of the stem cell therapy might be due to its modulation of inflammatory factors.