We evaluated the potential therapeutic use of exogenous human bone marrow-derived mesenchymal stem cells (hBM-MSCs) in an experimental rat model of necrotizing enterocolitis (NEC). Thirty-six newborn Sprague-Dawley rats were randomly divided into three groups: NEC, NEC + hBM-MSC, and a control (control and control + hBM-MSC). NEC was induced by enteral formula feeding, exposure to hypoxia-hyperoxia, and cold stress. After NEC was induced, iron-labeled hBM-MSCs were administered by intraperitoneal injection. All pups were killed on the fourth day following injection, and the terminal ileum was excised for a histopathological and immunohistochemical evaluation. The pups in the NEC + hBM-MSC group showed significant weight gains and improvements in their clinical sickness scores (p < 0.01). Bowel damage severity observed in the histopathological evaluation was significantly lower in the NEC + hBM-MSC group than that in the NEC group (p = 0.012). The number of MSCs homing to the bowel was significantly higher in the NEC + hBM-MSC group than that in the control + hBM-MSC group. In conclusion, this is the first study that has evaluated the effectiveness of hBM-MSCs in a neonatal rat NEC model. MSCs reduced histopathological damage significantly.