Bothersome gastrointestinal (GI) signs/symptoms, including abdominal pain, distension, nausea, and flatulence, are common in children. A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) is frequently recommended for children with GI symptoms. Currently, there are no studies on the effect of FODMAPs in healthy schoolchildren. In this cross-sectional study, schoolchildren reported an association between FODMAPs and GI symptoms through a standardized questionnaire and images of 20 common staples known to be rich in FODMAPs. A total of 208 schoolchildren aged 8–18 years old participated. A proportion of 38.0% of children reported GI symptoms, with abdominal pain (33%) being the most common complaint followed by abdominal distension (24%) and nausea (23%). The majority of children who reported intolerances to FODMAP-containing foods were intolerant to less than two food groups (76%). While vegetables and legumes (26%), particularly black beans (11%) and onions (7%), emerged as the most common group of triggers, milk (12%) stood out as the single food most frequently associated with GI symptoms. In conclusion, there was a high prevalence of FODMAPs intolerance among schoolchildren. Larger studies are recommended to confirm these findings and to inform possible dietary interventions to reduce the effect of FODMAPs on schoolchildren.