In the current experiment, we investigated the immune-modulatory potential of mesenchymal stem cells (MSCs) and conditioned media (CM) in attenuating of chronic asthmatic changes in a rat model. Male rats were divided into control (C) and ovalbumin-sensitized (S) groups, which further allocated into three subgroups; rats received systemically 50 μl volume of PBS (C and S groups), CM (CSV and SSV groups) and rats received intravenous infusion of 2 × 106 bone marrow-derived mesenchymal stem cells (rBMMSCs) (CCV and SCV groups). Two weeks later, the expression of interleukin (IL)-4, IL-13, and IL-10, miRNA133, and miRNA155 was measured by real-time PCR. Pathological changes and the recruitment of rBMMSCs into pulmonary parenchyma were evaluated by histopathological and immunofluorescence analyses, respectively. The systemic injection of rBMMSCs, but not CM, decreased the levels of IL-4, IL-13, IL-10, miRNA133, miRNA155 and reduced pathological changes in sensitized rats as compared with other sensitized groups (p < 0.001 to p < 0.05). rBMMSCs transmigrated to lung tissue in cell-administrated rats, albeit intensity of asthmatic changes, in turn, affected the amount of recruited cells. Collectively, our data suggest the potential role of MSCs, but not CM, in reducing pathological changes possibly via the modulation of miRNA133 and miRNA155 during asthmatic changes.