BACKGROUND: Evidence from studies in adults documents that fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) may be triggers of symptoms in individuals with functional abdominal pain disorders (FAPDs). However, in children, the evidence is very limited. We aim to assess the effects of a low-FODMAP diet compared with a regular diet for the management of children with FAPDs. METHODS: We will perform a randomized, quadruple-blinded, controlled trial. Seventy-four children aged 8 to 18 years with a FAPD (Irritable Bowel Syndrome or Functional Abdominal Pain-Not Otherwise Specified), diagnosed according to the Rome IV criteria, will be randomly allocated to receive either a low-FODMAP diet or a regular diet for 4 weeks. The primary outcome will be the percentage of the responders, defined as the participants who have at least 30% improvement in abdominal pain intensity on a Visual Analogue Scale (VAS) during the last week of the trial compared with baseline, that is at least equal to the Reliable Change Index (≥ 25 mm change on VAS). Other outcomes will include changes in stool consistency, abdominal pain frequency, total scores on the Gastrointestinal Symptom Rating Scale, KIDSCREEN-10 Index and World Health Organization Five Well-Being Index, child's school attendance and parents' work absenteeism, and BMI-for-age z-score. Compliance, tolerability of the low-FODMAP diet, and adverse events also will be evaluated. Each FAPD subtype will be assessed separately. DISCUSSION: There is a need for high-quality evidence regarding the dietary management of children with FAPDs. This randomized controlled trial (RCT) of rigorous methodological design will help to establish the effectiveness, if any, of a low-FODMAP diet for the management of FAPDs in the pediatric population. The findings of this RCT will assist with the development of guidelines and influence the direction of further research. TRIAL REGISTRATION: NCT04528914 Data and protocol version identifier: 24/08/2020.