This study aimed to investigate the diagnostic potential of serum high-mobility group box 1 (HMGB1) in neonatal encephalopathy (NE). A retrospective study was conducted, analyzing 216 neonates diagnosed with NE. The neonates were divided into two groups based on their outcomes at 28 days. Serum HMGB1 levels were compared between the two groups. ROC analysis was used to determine the predictive value of HMGB1. At 28 days, 174 infants had a good prognosis, while 42 had a poor prognosis. Infants with a poor prognosis had higher serum HMGB1 concentrations within 24 h of birth. Multifactorial analysis revealed that extremely preterm birth, extremely low birth weight, an Apgar score of 0-3 at 5 min, premature rupture of membranes by the mother, moderate to severe NE, and serum HMGB1 > 6.14 ng/mL are independent risk factors for poor prognosis. HMGB1 has predictive value for short-term prognosis with an area under the curve of 0.79. Elevated HMGB1 levels in the acute phase of NE are associated with poor short-term neonatal outcomes. The decrease in HMGB1 concentrations over time correlates with a good prognosis; whereas an increase suggests a poor prognosis. Early measurement of serum HMGB1 could aid in the prognostic assessment of neonates with NE. Although serum HMGB1 has emerged as a potential predictor of neonatal outcomes in neonatal encephalopathy, the relationship of HMGB1 levels to neonatal encephalopathy severity remains unclear. The current results demonstrate that infants with a poor prognosis had higher serum HMGB1 concentrations within 24 h of birth. Importantly, elevated serum HMGB1 levels in the acute phase of neonatal encephalopathy are associated with poor short-term neonatal outcomes. Our findings reveal the clinical values of HMGB1 in the prediction of neonatal outcomes in NE patients.