Ischemic stroke remains one of the leading causes of death worldwide, thereby highlighting the urgent necessary to identify new therapeutic targets. Deoxyhypusine hydroxylase (DOHH) is a fundamental enzyme catalyzing a unique posttranslational hypusination modification of eukaryotic translation initiation factor 5A (eIF5A) and is highly involved in the progression of several human diseases, including HIV-1 infection, cancer, malaria, and diabetes. However, the potential therapeutic role of pharmacological regulation of DOHH in ischemic stroke is still poorly understood. Our study first discovered a natural small-molecule brazilin (BZ) with an obvious neuroprotective effect against oxygen-glucose deprivation/reperfusion insult. Then, DOHH was identified as a crucial cellular target of BZ using HuProt™ human proteome microarray. By selectively binding to the Cys232 residue, BZ induced a previously undisclosed allosteric effect to significantly increase DOHH catalytic activity. Furthermore, BZ-mediated DOHH activation amplified mitophagy for mitochondrial function and morphology maintenance via DOHH/eIF5A hypusination signaling pathway, thereby protecting against ischemic neuronal injury in vitro and in vivo. Collectively, our study first identified DOHH as a previously unreported therapeutic target for ischemic stroke, and provided a future drug design direction for DOHH allosteric activators using BZ as a novel molecular template. Small-molecule brazilin shows significant neuroprotective effect against ischemic cerebral injury in vitro and in vivo. DOHH is identified as a crucial cellular target of brazilin via directly binding to Cys232. Brazilin allosterically activates DOHH conformation to promote a unique eIF5A hypusination and further induces mitophagy to exert neuroprotective effect. • Brazilin is the first DOHH allosteric activator for ischemic cerebral injury. • Cys232 is a crucial small-molecule binding site for DOHH allosteric activation. • DOHH/eIF5A hypusination signaling promotes mitophagy for neuronal cell protection. • DOHH is a promising pharmacological therapeutic target against ischemic stroke.