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.