As an important micronutrient, selenium (Se) plays many essential roles in immune response and protection against pathogens in humans and animals, but underlying mechanisms of Se-based control of salmonella growth within macrophages remain poorly elucidated. In this study, using RNA-seq analyses, we demonstrate that Se treatment (at an appropriate concentration) can modulate the global transcriptome of chicken macrophages HD11. The bioinformatic analyses (KEGG pathway analysis) revealed that the differentially expressed genes (DEGs) were mainly enriched in retinol and glutathione metabolism, revealing that Se may be associated with retinol and glutathione metabolism. Meanwhile, Se treatment increased the number of salmonella invading the HD11 cells, but reduced the number of salmonella within HD11 cells, suggesting that enhanced clearance of salmonella within HD11 cells was potentially modulated by Se treatment. Furthermore, RNA-seq analyses also revealed that nine genes including SIVA1, FAS, and HMOX1 were differentially expressed in HD11 cells infected with salmonella following Se treatment, and GO enrichment analysis showed that these DEGs were mainly enriched in an extrinsic apoptotic signaling pathway. In summary, these results indicate that Se treatment may not only affect retinol and glutathione metabolism in macrophages, but could also inhibit salmonella-induced macrophage apoptosis via an extrinsic apoptotic signaling pathway involving SIVA1.