Gene transcription in bacteria is mainly triggered by sigma factors (σ factors), such as rpoE. Bacterial ncRNAs are key players in reprogramming protein transcription when the environment changes. In our experiment, under the stress of ampicillin, the ncRNA transcriptomes of Salmonella enterica serovar Typhi wild-type strain (WT) and rpoE-deficient strain (ΔrpoE) were sequenced and analyzed, and four ncRNAs were selected to be verified by qRT-PCR. Of the ncRNA transcripts tested, 57 ncRNAs were found to have significantly different expressions (fold changes > 2) in ΔrpoE compared to WT, with 31 being upregulated and 26 being downregulated. The expression levels of the four ncRNAs verified preliminarily by subsequent qRT-PCR showed consistency with the sequencing data. Our study revealed the differences in ncRNA expression profiles between Salmonella enterica serovar Typhi WT and ΔrpoE under ampicillin stress. The four ncRNAs identified by qRT-PCR and their associated signaling pathways may be related to the envelope stress and antibiotic susceptibility of Salmonella enterica serovar Typhi.