The aim of the study was to assess the prevalence of joint hypermobility (JH) among school children with and without functional gastrointestinal disorders (FGIDs). School children completed validated Rome III questionnaires to diagnose FGID. Each child diagnosed with an FGID was matched for age and sex with a healthy control. The prevalence of JH in both groups was compared. A total of 654 school children participated in the study. One hundred forty-eight (22.6%) children were diagnosed with an FGID. Data from 136 FGIDs and 136 healthy controls were analyzed. Joint laxity was assessed to establish the Beighton score (≥4 was considered JH). There was no significant difference in JH between children with and without diagnoses of FGIDs odds ratio (OR) 1.03 (95% confidence interval [CI]: 0.59–1.81, P = 0.89). Multivariate analysis showed that younger age OR 2.31 (95% CI: 1.30–4.10, P = 0.004) and female sex OR 2.27 (95% CI: 1.22–4.24, P = 0.009) were significantly associated with JH. JH is equally prevalent in school children with and without FGIDs.