Ischemic stroke currently lacks evidence-based neuroprotective agents, primarily due to the challenge of timely intervention, which often occurs after the onset of irreversible neuronal damage. To address this, this study investigates the PARthanatos pathway, a form of regulated cell death triggered by DNA damage. Utilizing MNNG-induced cellular PARthanatos models, we screened a library of 2,939 traditional Chinese medicine monomers and identified Bruceine E, a natural product derived from Brucea javanica (bitterwood), as a potent inhibitor of PARthanatos at nanomolar concentrations, acting via the inhibition of PARP-1 overactivation. Bruceine E effectively prevents the accumulation of PAR-modified proteins, mitigates mitochondrial membrane potential collapse, and inhibits AIF nuclear translocation. Mechanistically, molecular docking, molecular dynamics simulations, surface plasmon resonance (SPR), and thermal stability assays demonstrate that Bruceine E interacts with the NAD + catalytic pocket of PARP-1 through six hydrogen bonds, exhibiting fast-binding and slow-dissociation kinetics. Furthermore, PARP1 overexpression rescue experiments confirmed that PARP1 overexpression markedly reversed the neuroprotective effect of Bruceine E, indicating that its pharmacological action is specifically dependent on PARP1 regulation. In a permanent distal middle cerebral artery occlusion (pdMCAO) model of C57BL/6 mice, a single intraperitoneal injection of 10 mg/kg Bruceine E administered 4.5 h after occlusion reduced infarct volume by approximately 80.2%, histological evidence confirmed that a single intraperitoneal administration of BE provided effective neuroprotection against ischemic brain injury.