The concentration of volatile organic compounds (VOCs) can inform about the metabolic condition of the body. In the small intestine of untreated persons with celiac disease (CD), chronic inflammation can occur, leading to nutritional deficiencies, and consequently to functional impairments of the whole body. Metabolomic studies showed differences in the profile of VOCs in biological fluids of patients with CD in comparison to healthy persons; however, there is scarce quantitative and nutritional intervention information. The aim of this study was to evaluate the effect of the supplementation of a gluten-free diet (GFD) with prebiotic oligofructose-enriched inulin (Synergy 1) on the concentration of VOCs in the urine of children and adolescents with CD. Twenty-three participants were randomized to the group receiving Synergy 1 (10 g per day) or placebo for 12 weeks. Urinary VOCs were analyzed using solid-phase microextraction and gas chromatography–mass spectrometry. Sixteen compounds were identified and quantified in urine samples. The supplementation of GFD with Synergy 1 resulted in an average concentration drop (36%) of benzaldehyde in urine samples. In summary, Synergy 1, applied as a supplement of GFD for 12 weeks had a moderate impact on the VOC concentrations in the urine of children with CD.