Background: Neutrophil infiltration and phenotypic transformation are believed to contribute to neuronal damage and clinical outcome in ischemic stroke. Emerging evidence suggests that HDAC2 is an epigenetic regulator of inflammatory cells. Here, we investigated whether miR-494 affects HDAC2-mediated neutrophil infiltration and phenotypic shift. Methods: The miR-494 levels in neutrophils from AIS patients were detected by real-time PCR. C57BL/6J mice were subjected to transient middle cerebral artery occlusion, and the N1/N2 neutrophil shift was examined. Cortical neurons were subjected to oxygen-glucose deprivation and stimulated with supernatant from differently treated neutrophils or were cocultured with neutrophils; neuronal injury was detected, and ChIP-Seq was performed to clarify which genes are the binding targets of HDAC2. Finally, a transwell assay was conducted to examine neutrophil migration. Results: Compared to the control subjects, AIS patients had increased neutrophil expression of miR-494, and in AIS patients, elevated miR-494 expression in neutrophils was a predictor of worse neurological outcomes. MiR-494 correlates with the upregulation of adhesion molecules in neutrophils of AIS patients. Systemically administered antagomiR-494 partly shifts neutrophils into the N2 phenotype in MCAO mice. AntagomiR-494-treated neutrophils exert a neuroprotective role in vitro. ChIP-seq revealed that HDAC2 targets multiple MMP genes in neutrophils of AIS patients. Further in vitro and in vivo experiments showed that antagomiR-494 repressed expression of MMP genes, including MMP7, MMP10, MMP13, and MMP16, to reduce the number of brain-infiltrating neutrophils by regulating HDAC2. Conclusion: MiR-494 may serve as an alternative predictive biomarker of the outcome of AIS patients, and antagomiR-494 treatment decreased the expression of multiple MMPs and the infiltration of neutrophils partly by targeting HDAC2.