Hypoxia–ischemia (HI)-induced perinatal encephalopathy frequently causes chronic neurological morbidities and acute mortality. Bone mesenchymal stem cell (BMSC) transplantation could potentially promote functional and anatomical recovery of ischemic tissue. In vitro hypoxic preconditioning is an effective strategy to improve the survival of BMSCs in ischemic tissue. In this study, cobalt chloride (CoCl2) preconditioned medium from BMSC cultures was injected into the left lateral ventricle of HI rats using a micro-osmotic pump at a flow rate 1.0 μl/h for 7 days. The protein levels of HIF-1α and its target genes, vascular endothelial growth factor and erythropoietin, markedly increased after CoCl2 preconditioning in BMSCs. In 7-week-old rats that received CoCl2 preconditioned BMSC medium, results of the Morris water maze test indicated ameliorated spatial working memory function following hypoxia-ischemia damage. Neuronal loss, cellular disorganization, and shrinkage in brain tissue were also ameliorated. Extracellular field excitatory postsynaptic potentials (fEPSPs) in the brain slices of 8-week-old rats were recorded; administration of CoCl2 preconditioned BMSC culture medium induced a progressive increment of baseline and amplitude of the fEPSPs. Immunohistochemical quantification showed that GluR2 protein expression increased. In conclusion, CoCl2 activates HIF-1α signals in BMSCs. CoCl2 preconditioned BMSC culture medium likely effects neuroprotection by inducing long-term potentiation (LTP), which could be associated with GluR2 expression. The paracrine effects of hypoxia preconditioning on BMSCs could have applications in novel cell-based therapeutic strategies for hypoxic and ischemic brain injury.