Severe intraventricular hemorrhage (IVH) in premature infants triggers reactive gliosis, causing acute neuronal death and glial scar formation. Transplantation of mesenchymal stem cells (MSCs) has often showed improved CNS recovery in an IVH model, but whether this response is related to reactive glial cells is still unclear. Herein, we suggest that MSCs impede the response of reactive microglia rather than astrocytes, thereby blocking neuronal damage. Astrocytes alone showed mild reactiveness under hemorrhagic conditions mimicked by thrombin treatment, and this was not blocked by MSC-conditioned medium (MSC-CM) in vitro. In contrast, thrombin-induced microglial activation and release of proinflammatory cytokines were inhibited by MSC-CM. Interestingly, astrocytes showed greater reactive response when co-cultured with microglia, and this was abolished in the presence of MSC-CM. Gene expression profiles in microglia revealed that transcript levels of genes for immune response and proinflammatory cytokines were altered by thrombin treatment. This result coincided with the robust phosphorylation of STAT1 and p38 MAPK, which might be responsible for the production and release of proinflammatory cytokines. Furthermore, application of MSC-CM diminished thrombin-mediated phosphorylation of STAT1 and p38 MAPK, supporting the acute anti-inflammatory role of MSCs under hemorrhagic conditions. In line with this, activation of microglia and consequent cytokine release were impaired in Stat1-null mice. However, reactive response in Stat1-deficient astrocytes was maintained. Taken together, our results demonstrate that MSCs mainly block the activation of microglia involving STAT1-mediated cytokine release and subsequent reduction of reactive astrocytes.