Neonatal bacterial meningitis is associated with substantial mortality and morbidity worldwide. Neonatal meningitis-causing Escherichia coli (NMEC) is the most common gram-negative bacteria responsible for this disease. However, the interactions of NMEC with its environment within the host are poorly understood. Here, we showed that a low level of leucine, a niche-specific signal in the blood, promotes NMEC pathogenicity by enhancing bacterial survival and replication in the blood. A low leucine level downregulates the expression of NsrP, a small RNA (sRNA) identified in this study, in NMEC in an Lrp-dependent manner. NsrP destabilizes the mRNA of the purine biosynthesis-related gene purD by direct base pairing. Decreased NsrP expression in response to low leucine levels in the blood, which is a purine-limiting environment, activates the bacterial de novo purine biosynthesis pathway, thereby enhancing bacterial pathogenicity in the host. Deletion of NsrP or purD significantly increases or decreases the development of E. coli bacteremia and meningitis in animal models, respectively. Furthermore, we showed that intravenous administration of leucine effectively reduces the development of bacteremia and meningitis caused by NMEC by blocking the Lrp-NsrP-PurD signal transduction pathway. This study provides a potential strategy for the prevention and treatment of E. coli-induced meningitis.