Introduction Emerging evidence suggests an association between obesity and Functional Gastrointestinal Disorders (FGIDs). Childhood obesity and FGIDs share many common features, such as high prevalence in the pediatric population, risk factors related to diet and lifestyle, gut microbiota impairments, and psychological distress. This narrative review aims to summarize the main evidence regarding FGIDs in childhood obesity, with a specific focus on the role of diet and its impact on the microbiota. Additionally, the review highlights potential common-ground solutions for preventing and managing both obesity and FGIDs. Methods A comprehensive PubMed search was conducted. Keywords used included terms related to children and adolescents, obesity, functional gastrointestinal disorders, and microbiota. Results The review emphasizes the importance of holistic, multidisciplinary approaches to managing symptoms. In addition to nutrition education, physical activity, and medical care, complementary strategies such as psychological interventions and personalized dietary modifications (e.g., low-FODMAP and fiber-enriched diets) are critical. Given the interplay between gut microbiota alterations, obesity, and FGIDs, microbiota modulation through probiotics, prebiotics, and integrative support shows significant promise. However, the variability in current evidence underlines the need for robust longitudinal studies to develop standardized protocols and maximize treatment efficacy. Conclusions Bridging gaps in knowledge and practice with an integrated, evidence-based framework could improve patient outcomes and deepen understanding of the complex relationship between metabolic and gastrointestinal health in children and adolescents.