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Ureaplasma parvumencephalitis is a rare disease with high mortality in the neonates. While the manifestations are atypical and identification of U. parvumis difficult, diagnosis would always be delayed. Metagenomic next-generation sequencing (mNGS) is a pre-hypothesis free technique which could theoretically detect all the microbes in a sample. Herein we report a case of U. parvummeningitis identified by mNGS in an extremely low birth weight neonate complicated with multi-system lesions. The patient was treated with erythromycin and ciprofloxacin, symptoms were relieved in the following days and the patient was transferred to treat complications after three weeks' therapy.