Purpose: We compared the health-related quality of life (HRQOL) of children and adolescents with functional abdominal pain disorders (FAPDs) and organic abdominal pain disorders (ORGDs). Methods: This was a single-center, cross-sectional, observational study. The PedsQL 4.0 generic cores scales parent proxy-report was administered to parents/caregivers of 130 and 56 pediatric patients with FAPDs and ORGDs respectively on their first visit. The self-reported pain intensity in the patients was assessed using a visual analog scale (VAS) and facial affective scale (FAS). Results: Irritable bowel syndrome was the most prevalent FAPDs, and the most prevalent ORGDs were reflux esophagitis (41.1%) and gastritis associated with Helicobacter pylori (21.4%). There was no difference in HRQOL among patients diagnosed with ORGDs and FAPDs (p>0.05). Patients with ORGDs and FAPDs had lower HRQOL Scale scores than healthy Brazilian and American children’s references, with a high proportion of children at risk for impaired HRQOL (p<0.0001). There was no difference in the VAS and the FAS scores between the ORGDs and the FAPDs. FAPDs had a higher prevalence of girls’ and couples’ disagreement (p<0.02), although poor school performance (p<0.0007) and bullying (p<0.01) were higher in patients with ORGD. Conclusion This study revealed that there was a difference in impaired HRQOL between patients with ORGDs and FAPDs. Thus, considering the high prevalence of chronic abdominal pain in children, a well-founded treatment plan is necessary for a multidisciplinary cognitive-behavioral Pain management program.