The intracellular pathogen
Salmonella enterica
serovar Typhimurium (
S
. Typhimurium) exploits host macrophage as a crucial survival and replicative niche. To minimize host immune response stimulated by flagellin, the expression of flagellar genes is downregulated during
S
. Typhimurium growth within host macrophages. However, the underlying mechanisms are largely unknown. In this study, we show that STM14_1285 (named AsiR), a putative RpiR-family transcriptional regulator, which is downregulated within macrophages as previously reported and also confirmed here, positively regulates the expression of flagellar genes by directly binding to the promoter of
flhDC
. By generating an
asiR
mutant strain and a strain that persistently expresses
asiR
gene within macrophages, we confirmed that the downregulation of
asiR
contributes positively to
S
. Typhimurium replication in macrophages and systemic infection in mice, which could be attributed to decreased flagellar gene expression and therefore reduced flagellin-stimulated secretion of pro-inflammatory cytokines IL-1β and TNF-α. Furthermore, the acidic pH in macrophages is identified as a signal for the downregulation of
asiR
and therefore flagellar genes. Collectively, our results reveal a novel acidic pH signal-mediated regulatory pathway that is utilized by
S
. Typhimurium to promote intracellular replication and systemic pathogenesis by repressing flagellar gene expression.