Panax notoginseng saponins (PNS), the main active ingredient of herbal medicine Panax notoginseng, has been generally applied for the therapy of cardiovascular and cerebrovascular diseases, especially for stroke. It is believed that PNS has obvious anti-inflammatory effect, however, the roles of PNS on microglia after stroke have not been completely explored and the underlying mechanism of microglia-mediated inflammation remains to be clarified. In this study, cerebral ischemia injury was induced by photothrombotic (PT) stroke in mice. Two days after operation, PNS administration alleviated ischemic brain injury by increasing grip strength, relieving neurological deficits, improving local cerebral blood flow, and reducing pathological damage in the brain cortex and hippocampus. Moreover, microglial activation occurred in the acute stage after stroke and mediated inflammation, whereas PNS administration could inhibit microglial activation and inflammation. Meanwhile, we firstly demonstrated that PKM2 expression was upregulated in the nucleus of activated microglia after stroke, which could be inhibited after PNS administration. We hypothesized that suppression of nuclear PKM2 upregulation in microglia along with downregulation of HIF-1α/PKM2/STAT3 signaling could partially underlie the potential anti-inflammatory mechanism of PNS against ischemic brain injury. Our findings offer some new standpoints about PNS against microglia-mediated inflammation after stroke. Despite strengths, this study has limitation. PKM2 is not specifically expressed by microglia, but could be expressed by neurons, vascular endothelial cells, etc. Here we only explored the effect of PKM2 on activated microglia, and we would further investigate the impact of PKM2 expressed in other cells on stroke outcome in the future.