Ureaplasma parvum (U. parvum) is common commensal in the female genitourinary tract. Despite U. parvum has been associated with chorioamnionitis, abortion, prematurity and perinatal complications, the invasive central nervous system (CNS) infection is rare in neonates. Diagnosis of U. parvum meningitis can be difficult for the atypical presentations and sterile cultures by conventional methods. Metagenomic next-generation sequencing (mNGS) could identify a broad range of human pathogens in a target-independent manner. Here, we performed mNGS to search for the infectious etiology in a term infant presenting with fever and seizure. U. parvum genome was identified by mNGS and further confirmed by PCR in the same cerebrospinal fluid (CSF) sample. As the quick and timely diagnosis, the baby was successfully treated with erythromycin for 4 weeks without complication. The clinical follow-up has showed that the physical and mental development are normal. In conclusion, mNGS may a promising diagnostic technology for U. parvum meningitis. As mNGS is able to identify diverse microbes in a single run, it could be a useful strategy to detection the clinical causative pathogens with atypical features in neonates.