Systemic administration of mesenchymal stem cells (MSCs) has been reported to improve neurological function in brain damage, including hypoxic–ischemic encephalopathy (HIE), though the action mechanisms have not been fully elucidated. In this study, the cells were tracked live using a Pearl Trilogy Small Animal fluorescence imaging system after human embryonic stem Cell-Derived MSCs (ES-MSCs) infusion for an HIE mouse model. ES-MSC–treated HIE mice showed neurobehavioral improvement. In vivo imaging showed similar sequential migration of ES-MSCs from lungs, liver, and spleen within 7 days in both HIE and normal mice with the exception of lungs, where there was higher entrapment in the HIE 1 h after infusion. In addition, ex vivo experiments confirmed time-dependent infiltration of ES-MSCs into the organs, with similar findings in vivo, although lungs and brain revealed small differences. ES-MSCs seemed to remain in the brain only in the case of HIE on day 14 after the cell infusion. The homing effect in the host brain was confirmed with immunofluorescence staining, which showed that grafted cells remained in the brain tissue at the lesion area with neurorestorative findings. Further research should be carried out to elucidate the role of each host organ’s therapeutic effects when stem cells are systemically introduced.