Neonatal hypoxic-ischemic encephalopathy (HIE) is a disorder mainly due to asphyxia during the perinatal period, and late diagnosis leads to high mortality. In this study, the expression of microRNA-199a (miR-199a) in HIE newborns was investigated, as well as its clinical significance in HIE diagnosis and prognosis. Circulating levels of S100B and NSE in HIE newborns were measured using enzyme-linked immunosorbent assay, and the expression of miR-199a was analyzed using quantitative real-time PCR. The diagnostic value of miR-199a, S100B and NSE was evaluated using the receiver operating characteristic (ROC) analysis, and their prognostic value was assessed by the evaluation of Gesell intellectual development of the HIE newborns. HIE newborns possessed significantly increased levels of S100B and NSE and decreased miR-199a (all P < 0.01). The Neonatal Behavioral Neurological Assessment (NBNA) score of HIE newborns was negatively correlated with S100B and NSE, while was positively correlated miR-199a. The ROC analysis results showed the diagnostic value of serum miR-199a, and the combined detection of miR-199a, S100B and NSE could obtained the highest diagnostic accuracy in HIE newborns. miR-199a expression was lowest in newborns with severe HIE, and it had diagnostic potential to distinguish HIE cases with different severity. Regarding the prognosis of neonatal HIE, the correlation of miR-199a, S100B, NSE with Gesell intellectual development was found in HIE newborns. The decreased miR-199a in HIE newborns serves as a potential diagnostic biomarker and may help to improve the diagnostic and prognostic value of S100B and NSE in neonatal HIE.