Background <p>Childhood obesity is a global concern, associated with various metabolic complications. Gut microbiota dysbiosis has been implicated in its pathogenesis. Synbiotics may improve metabolic health by modulating gut microbiota.</p> Objective <p>To evaluate the effects of synbiotic supplementation on lipid profiles, fasting blood glucose (FBG), insulin, and alanine aminotransferase (ALT) in children with obesity.</p> Methods <p>This randomized, double-blind, placebo-controlled trial (April 2024-June 2025), children aged 7–18 years with obesity received either a new freeze-dried synbiotic (10&#xa0;g inulin from Thai Jerusalem artichoke plus <i>Bifidobacterium animalis</i> and <i>Lactobacillus paracasei</i>, 10⁷ CFU each) or a placebo (isocaloric maltodextrin) daily for 3 months. Both groups received the same lifestyle modification counseling. Anthropometric measurements, dietary intake, physical activity, and metabolic parameters were assessed at baseline and month 3.</p> Results <p>Sixty children were enrolled; 57 completed the study. High-density lipoprotein cholesterol (HDL-C) significantly increased in the synbiotic group compared to controls [median change: 0.34 (-0.16, 1.35) vs. -0.84 (-1.35, -0.33) mg/dL, <i>P</i> = 0.001], after adjusting for baseline. No significant changes were observed in BMI z-score or other metabolic parameters. Furthermore, there were no significant differences in dietary intake or physical activity levels between groups at the 3-month follow-up.</p> Conclusions <p>Synbiotic supplementation significantly improved HDL-C in children with obesity. These results suggest that synbiotics may serve as an adjunctive nutritional intervention for managing metabolic health in childhood obesity.</p> Trial registration <p><a href="https://www.thaiclinicaltrials.org/">https://www.thaiclinicaltrials.org/</a> (TCTR20240321005).</p>