Extracellular glutamate contributes to brain damage in ischemia. Under physiological conditions, glutamate transporters are responsible for regulating its intracellular/extracellular concentrations in the brain. However, how the extracellular glutamate is regulated in ischemia remains unclear. Here, we showed that the sonic hedgehog (SHH)–Smoothened (SMO)–GLT-1 pathway controlled extracellular glutamate and blocking SMO reduced ischemic brain damage in rodents. SHH was quickly released in a rodent model of ischemia, and activation of its pathway was associated with neuronal damage. Inhibiting SMO, the mediator of SHH signaling, maintained GLT-1 membrane expression, lowered extracellular glutamate, reduced infarct volume, and improved neurological functions in mice. Mechanistically, SHH suppressed GLT-1 membrane expression via PKCα phosphorylation of serine-562 on GLT-1. Last, administration of NVP-LDE225, an FDA-approved SMO antagonist used for cancer treatment in clinic, had protective effects in mice and cynomolgus monkeys subjected to ischemia. Together, these results suggest that SMO could be targeted for treating glutamate toxicity in ischemia.