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Aims: Status epilepticus (SE) is the most common neurological emergency in pediatric patients. This study aimed to screen for prognostic biomarkers of SE in the cerebrospinal fluid (CSF) using metabolomics. Methods: Ultra‐performance liquid chromatography quadrupole time‐of‐flight tandem mass spectrometry (UPLC‐QTOF‐MS) was conducted to identify prognostic biomarkers in CSF metabolomics by comparing the poor outcome group (N = 13) with the good outcome group (N = 15) of children with SE. Differentially expressed metabolites were identified using Mann–Whitney U test corrected by Benjamini‐Hochberg and partial least squares discriminant analysis (PLS‐DA). Results: The PLS‐DA model identified and validated significant metabolic differences between the poor and good outcome groups of children with SE (PLS‐DA with R2Y = 0.992 and Q2 = 0.798). A total of 49 prognosis‐related metabolites were identified. Of these metabolites, 20 including glutamyl‐glutamine, 3‐iodothyronamine, and L‐fucose had an area under the curve (AUC) ≥ 80% in prognostic prediction of SE. The logistic regression model combining glutamyl‐glutamine and 3‐iodothyronamine produced an AUC value of 0.976, with a sensitivity of 0.863 and specificity of 0.956. Pathway analysis revealed that dysregulation of the citrate cycle (TCA) and arginine biosynthesis may contribute to poor SE prognosis. Conclusions: This study highlighted the prognosis‐related metabolomic disturbances in the CSF of children with SE and identified potential prognostic biomarkers. A prognostic prediction model combining glutamyl‐glutamine and 3‐iodothyronamine with high predictive value was established. [ABSTRACT FROM AUTHOR]