Purpose: The aim of this study was to compare the frequency of functional gastrointestinal diseases (FGIDs) in juvenile idiopathic arthritis (JIA) patients with healthy control children. Materials and Methods: This case-control study includes 193 children with JIA followed-up between October 2012 to April 2019 and 139 healthy control children. Demographic features, disease characteristics, treatment modalities were collected retrospectively. Laboratory parameters were recorded at the study enrollment. FGIDs diagnosis were assessed by utilizing Rome IV criteria. Gender, age at disease onset, laboratory parameters, treatment modalities, and clinical status of the disease were compared between the groups. Results: The mean age at study enrollment was 12.05±4.05 and 9.01±3.97 years in children with JIA and healthy control group, respectively. The frequency of FGIDs was significantly higher in JIA patients (13.7%, n=19) than in healthy control group (21.8%, n=42). There was no statistical significance between JIA patients and healthy control group in terms of FGIDs subtypes. Demographic and clinical parameters did not differ between JIA patients grouped according to FGIDs presence. Conclusion: FGIDs is more frequent in JIA patients than healthy controls. Further studies are needed to support our results.