Purpose: Recently, great interest has been focused on dietary fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) for the treatment of functional abdominal pain (FAP). Several meta-analyses, including those on the adult population, have been published, potentiating its role. However, pediatric studies are scarce. We aimed to evaluate the effect of a low-FODMAP diet on the severity of FAP in children. Methods: This clinical trial included 50 patients aged 3–18 years with irritable bowel syndrome and FAP that were not otherwise specified. The patients were instructed to receive a low FODMAP diet guided by a dietitian. The primary outcome was the percentage of responders after 2 months of dietary intervention compared with baseline. Other outcomes included changes in stool consistency and quality of life (QoL) scores using the KIDSCREEN-10 questionnaire, and weight-for-age z-scores. Results: After the dietary intervention, 74% of patients showed more than 30% lower pain intensity, as examined using the Wong-Baker Faces pain rating scale. Their QoL significantly improved, and patients have gained weight. Conclusion A low FODMAP diet can improve pain intensity and QoL among children with functional abdominal pain, with no detrimental effects on body weight.