Staphylococcus epidermidis (S. epidermidis) is one of the primary pathogens in postoperative endophthalmitis, which is a devastating complication of cataract surgery and often results in irreversible visual loss and even blindness. Meanwhile, it is the most frequently isolated commensal bacterium in the healthy conjunctiva. In this study, we investigated the differentially expressed genes (DEGs) of S. epidermidis isolated from the patients with postoperative endophthalmitis and the healthy conjunctiva to predict their functions and pathways by Illumina high-throughput RNA sequencing. Using genome-wide transcriptional analysis, 281 genes (142 upregulated and 139 downregulated genes) were found to be differentially expressed (fold change ≥ 2, p ≤ 0.05) in the strains from endophthalmitis. Ten randomly selected DEGs were further validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). GO enrichment analysis suggested that more DEGs were associated with the thioredoxin system and iron ion metabolism. KEGG pathway analysis revealed that more DEGs were associated with the pathways of the two-component system and pyruvate metabolism. Moreover, the gene SE1634 code for staphylococcal toxin was significantly upregulated in S. epidermidis strains of the endophthalmitis, which might be directly responsible for the pathogenesis of endophthalmitis. In conclusion, this research is helpful for further investigations on genes or pathways related with the pathogenesis and therapeutic targets of S. epidermidis endophthalmitis.