[Abstract] Objective: The core genes of neuroinflammation mediated by microglia in sepsis-associated encephalopathy (SAE) were screened by bioinformatics analysis and verified by cellular experiments in vitro. Methods: The genome-wide blood transcriptional profiling dataset GSE65682 of sepsis patients and the microarray whole transcriptome profiling dataset GSE103156 of lipopolysaccharide (LPS) treated BV2 microglia cells were obtained from gene expression omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) was used to screen the modules significantly related to clinical diagnosis of sepsis in GSE65682 dataset, and then was intersected with the differentially expressed genes (DEGs) in microglia before and after LPS processing in GSE103156 dataset. Gene ontology (GO) and Jingdu gene and genome encyclopedia (KEGG) were used to analyze the functional enrichment. The protein-protein interaction network was constructed by STRING, and the core genes were screened by Cytoscape and Lasso regression analysis. The in vitro microglial activation model induced by LPS was established, and real-time fluorescence quantitative PCR (qPCR) was used to analyze gene expression. HDAC9 was overexpressed in microglia using the lentiviral vector method, and Western blot was employed to detect the inflammation related molecule expression. Results: A total of 332 genes belonging to 9 modules of GSE65682 dataset were identifed closely related to the clinical diagnosis of sepsis by WGCNA analysis. 1272 DEGs of microglia before and after LPS stimulation in GSE103156 dataset were obtained by Limma analysis, and 18 overlapping genes were obtained. Four hub genes were screened by Lasso regression analysis, which were GPR183, HDAC9, NADK and LRRC25 respectively. QPCR results confirmed that in the microglial inflammatory activation model stimulated by LPS, the expression of GPR183 and HDAC9 at mRNA level was down-regulated, while the expression of LRRC25 was up-regulated, but there was no significant change in NADK expression. Western blot suggested that HDAC9 overexpression promoted the LPS induced expression of pro-inflammatory factor IL-1β and iNOS, and elevated the JAK1-STAT3 phosphorylation in microglia. Conclusion: In this study, four key genes of neuroinflammation mediated by SAE microglia were screened by bioinformatics, and it was preliminarily confirmed that HDAC9 has pro-inflammatory activity in microglia, which may provide new ideas and data for further mechanism study of SAE.