RNase E-mediated RNA processing and degradation are involved in bacterial adaptation to environmental changes. The RraA regulatory protein, which is highly conserved in γ-proteobacteria, differentially modulates RNase E activity. Recent studies have revealed the association of Salmonella enterica serovar Typhimurium RNase E (STRNase E) with bacterial pathogenicity; however, the molecular mechanisms are unknown. Here, we show that the expression levels of STRraA, a protein regulator of STRNase E activity, affect S. Typhimurium pathogenicity. RNA-sequencing and RT-PCR analyses indicated positive effects of STRraA levels on the abundance of mRNA species from class II flagellar operons. Primer extension analysis further identified STRraA-regulated STRNase E cleavage in the 5' untranslated region of fliDST mRNA. The cleavage affected the stability of this polycistronic mRNA, suggesting that STRraA protects fliDST mRNA from STRNase E cleavage, leading to enhanced flagellar assembly. Accordingly, STRraA positively regulated flagellar assembly and motility. In addition, STrraA-deleted cells showed decreased invasion ability and cytotoxicity in infection of human cervical epithelial carcinoma cells and reduced mortality in a mouse infection model compared to wild-type cells. These results support an active role of STRraA in RNase E-mediated modulation of pathogenesis in S. Typhimurium.