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Numerous investigations indicate that cyclosporine A (CsA) significantly influences the prevention or progression of Alzheimer’s disease (AD) through various mechanisms. The precise pathways by which CsA, an inhibitor of calcineurin (CN) and peptidyl-prolyl isomerase A (PPIA), operates remain incompletely elucidated. In this study, we explored the effects of CsA, a widely utilized immunosuppressive agent, on the gene expression of various factors related to inflammation, cell adhesion, intercellular communication, and apoptosis in SH-SY5Y cells. We employed the semi-quantitative real-time PCR (RT-qPCR) method for gene expression analysis to assess these effects. Furthermore, network pharmacology was utilized to identify the potential targets of CsA and to further analyze. Our results demonstrated that CsA enhances the mRNA levels of most factors examined, including IL1B, S100A9, CD147, TREM2, LRP1, MAPK1, MAPK14, GSK3B, Dynamin 1, Dynamin 3, NLRP3, NLRP1, CASPASE 3, CASPASE 1, AIFM1, and STAT3. At the same time, it suppresses the mRNA levels of PPIA, TLR2, TLR4, PYCARD, RAGE, and BCL2. The network pharmacology analysis revealed seven target genes overlapping our experimental findings (PPIA, S100A9, TLR4, STAT3, MAPK1, MAPK14, and BAX). Our results suggest that CsA modulates gene expression in SH-SY5Y cells, with the potential for either beneficial/ harmful effects on cellular function, depending on the specific roles of the assessed genes.