Background: Metagenomic next generation sequencing (mNGS) is becoming an increasingly available diagnostic method used to identify a broad range of pathogens. However, the optimal role of mNGS in clinical diagnostic schema remains uncertain, especially in pediatric patients suspected central nervous system (CNS) infection and treated with empirical antibiotic. The purpose of this study was to investigate the usefulness of cerebrospinal fluid (CSF) mNGS in the pediatric patients.Methods: We performed a retrospective review of suspected CNS infection patients who had CSF mNGS test from April 2019 to December 2020. Results and clinical impact of mNGS test were collected. We investigated the usefulness of CSF mNGS in clinical impact and diagnosis. Results: We enrolled 57 pediatric patients with empirical treatment. A total of 39 CNS infection patients were diagnosed, and 27 patients were identified by mNGS that only 2 of 27 were co-identified by CSF culture. In all of the patients, 75.4% (45 cases) had changed (addition or de-escalation) in antimicrobial therapy according to the results of the mNGS test. By each CSF mNGS test as a whole, the positive and negative percent agreement were 69.2% (95% CI: 54.1-84.4%) and 61.1% (95% CI: 36.2-86.1%), respectively, and true negatives of negative mNGS tests were 50% (95% CI: 27.3 – 72.7%).Conclusion: In this study, CSF mNGS test improved the diagnosis of neurologic infections and adjusted antibiotic therapy in the vast majority of cases. Consequently, for patients with empirical treatment, CSF mNGS should be used more in pathogen diagnosis and clinical therapy.