We performed a cross-sectional study. In spring 2019, 1,594 students (mean age 12.87 years) completed a questionnaire on gastrointestinal symptoms, smartphone use, Quality of Life (QoL), dietary habits, and physical activity. Based on the Rome IV criteria, 30.9% of participants met the symptom-based criteria for FGIDs and 8.9% experienced ≥2 disorders simultaneously. Well-being was less frequently reported by children with FGIDs than others (29.0% vs. 48.2%; p < 0.001). Participants addicted to smartphones reported low than others well-being (18.0% vs. 25.8%; p < 0.001), they also showed higher prevalence of FGIDs [Odds Ratio (OR), 1.98; 95% Confidence Interval (CI), 1.47-2.68; p < 0.001]. Among dietary habits, skipping breakfast (OR, 1.50; 95% CI, 1.09-2.05; p = 0.01) and low fruit consumption (OR, 1.66; 95% CI, 1.172.36; p = 0.005) were more frequent in participants with FGIDs. FGIDs are common in pediatric populations. FGIDs have an impact on QoL. Some dietary habits and physical activity are associated with these disorders. Smartphone addiction was found to be associated with FGIDs.