Background <p>Numerous studies have identified disruptions in the gut microbiota of patients with migraine, and the role of the gut–brain axis in the pathogenesis and development of migraine has been established. The incidence of migraine in children increases with age, yet the intestinal microbiota in pediatric migraine has been inadequately investigated. Therefore, we aim to investigate the composition, functional characteristics, and metabolite profiles of the gut microbiota in children with migraine.</p> Methods <p>We recruited 30 children with migraine and 30 healthy controls aged 5–14 years from Hebei Province, China, and collected 60 fresh fecal samples. Metagenomic sequencing was performed to obtain species abundance profiles and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations of gene sequences. Non-targeted metabolomic analysis was applied to assess differential changes in gut microbiota metabolites between children with migraine and healthy controls.</p> Results <p>The abundance of gut microbiota species was significantly reduced in children with migraine (<i>P</i> = 0.001), and was associated with migraine presence (R² = 0.051, <i>P</i> = 0.001). Bacteria within <i>Pseudomonadota</i> were significantly enriched in the gut flora of children with migraine, with <i>Escherichia coli</i> being the most abundant species. The propionic acid, the arginine and proline metabolism pathways were significantly upregulated in children with migraine (<i>P</i> &lt; 0.05). In contrast, the porphyrin metabolism pathway, amino acid biosynthesis pathway, and arginine biosynthesis pathway were significantly down-regulated (<i>P</i> &lt; 0.05). The intestinal lipopolysaccharide biosynthetic pathway showed diagnostic potential for pediatric migraine, with an Area Under the Curve (AUC) of 0.75 (95% CI: 0.63–0.87). Intestinal metabolites were also dysregulated in children with migraine; notably, Docosahexaenoyl Ethanolamide (DHEA) and kynurenic acid were significantly depleted (<i>P</i> &lt; 0.05).</p> Conclusion <p>This study revealed an association between gut microbiota and its metabolite in children with migraine, suggesting that the potential pathogenic role of gut microbiota may be mediated by the functions of <i>Pseudomonadota</i> and <i>Escherichia coli</i> and by the levels of metabolites derived from them. Furthermore, this study provides strong evidence for the diagnostic potential of kynurenic acid in pediatric migraine and supports future targeted metabolite research.</p> Graphical Abstract <p></p>