The ischemic brain can dialogue with peripheral tissues through the immune system. Ginkgo biloba extract (EGb) was used to regulate various neurological disorders; however, the impact of EGb on ischemic stroke is still unclear. Here, we aimed to investigate whether immunomodulation has participated in the beneficial effects of EGb on ischemia/reperfusion (I/R) brain injury. Mice were orally administered with EGb once daily for 7 days before the induction of I/R. Neurobehavioral scores, infarct volume, and brain inflammation were determined. The proportion of CD4+ T cells was detected by flow cytometry. EGb significantly lowered neurobehavioral scores, infarct volume, and the level of inflammatory cytokines in I/R mice. Interestingly, EGb altered the proportion of CD4+ T cells, particularly increasing the proportion of Treg cells. Depletion of Treg cells weakened the neuroprotective effects of EGb on ischemic stroke; furthermore, EGb decreased the expression of HIF-1α and HK2 and promoted the differentiation of Treg cells in vitro. EGb suppressed the HIF-1α/HK2 signaling pathway to promote the differentiation of Treg cells and ameliorate ischemic stroke in mice. The expansion effect of EGb on Treg cells could be exploited as part of future stroke therapy.