High concentrations of neutrophil degranulation products in the plasma and thrombi are poor prognostic indicators in patients with acute ischemic stroke (AIS). This study aimed to identify candidate effectors capable of mediating neutrophil degranulation post-AIS, and to reveal their underlying epigenetic mechanisms. Microarrays and ChIP-seq were applied to analyze the neutrophils of patients with AIS. Cerebral ischemia was induced in C57/BL6 mice by middle cerebral artery occlusion (MCAO). Lipopolysaccharide was used to induce inflammation in HL-60 Cells. Protein and mRNA levels were assessed using flow cytometry, ELISA, western blotting, and RT-PCR. Degranulation was identified as a significant pathway in the neutrophils of patients with AIS, while Rho GTPase and the SNARE complex also showed importance. HDAC2 differentially binds to genes involved in neutrophil degranulation in patients with AIS. SYT9, SH3BP1, and STXBP1 were identified in two sequencing experiments, for which HDAC2 bound to their promoter, intron, and upstream regions, respectively. Consistently, candidate degranulation effectors and products showed substantially increased expression and co-localization in the neutrophils of thrombi obtained from patients with middle cerebral artery stenosis with poor prognosis, a mouse model of MCAO, and an HL-60 cell-based model of inflammation. Knockdown of SYT9, SH3BP1, and STXBP1 impaired primary granule release in vitro, whereas HDAC2 activity was decreased following LPS induction and ischemic stroke in mice. Furthermore, HDAC2 inhibition upregulated SYT9, SH3BP1, and STXBP1. Our findings suggest that these three molecules may be indispensable in the process of neutrophil degranulation following AIS, and are targeted by HDAC2, paving the way for the development of new drugs.