Dietary patterns may have a role in the prevention of functional gastrointestinal disorders (FGIDs). The current study aimed at examining the association between FGIDs and adherence to the Mediterranean diet (MD) among elementary school children (ESC), as well as high school students (HSS). In a prospective cohort study, data from 1116 subjects (387 ESC and 448 HSS) aged 6–18 years were collected. FGID identification was based on the Questionnaire on Pediatric Gastrointestinal Symptoms-Rome III (QPGS-RIII). Adherence to the MD was assessed using the KIDMED Index. Full data were available on 835/1116 questionnaires. Based on Rome III criteria, 184/835 participants (22%) were identified with FGID (122 (66%) with functional constipation (FC)). The prevalence of FGIDs (p = 0.001) was significantly higher in HSS (13–18 years). The KIDMED score in the cohort was 5.7 ± 2.5. Subjects with FGIDs demonstrated a lower KIDMED score compared to the non-FGID group, both in the cohort, as well as in the ESC and HSS subgroups (FGID vs. non-FGID: p = 0.001, p = 0.007, and p = 0.032, respectively). Multivariate analysis highlighted the KIDMED score as a significant predictor of FGIDs and FC after controlling for the age subgroups. We conclude that good adherence to the MD is associated to lower prevalence of FGIDs, while adolescents display a significantly higher prevalence of FGIDs compared to children.