Background: Celiac disease (CD) is a common autoimmune disorder that presents intestinal and extra-intestinal symptoms. It is also associated with cardiovascular diseases and malignancies, and mortality risk. The only way to control the disease is to follow a strict gluten-free diet (GFD) for the rest of life. Objectives: This survey aimed to investigate GFD non-adherence and causes in the pediatric setting. Methods: In this study, 187 children aged between 2.5 to 14 years old with a confirmed diagnosis of CD at least for a year were studied using a questionnaire-based interview in a census study between 2018 to 2019 in a referral center in southern Iran. Results: About 40% of children adhered to a GFD poorly. This group significantly complained of more symptoms than the group with high adherence. Improper access was the most important cause of non-adherence to a GFD. Among the analyzed variables, the mean current weight and at the time of diagnosis, along with the mean current body mass index (BMI) and at the time of diagnosis, were statistically significant, which were respectively lower and higher in the non-adherent group. However, IgA anti-tTG and histopathologic examination did not change remarkably. Furthermore, no significant relationship was found between following a GFD and age, age at the time of diagnosis, gender, and parental educational status. Conclusions: According to our results, inaccessibility, high costs, and lack of food labeling were the primary reasons for non-adherence to GDF. Therefore, to increase compliance, easy access to GFD with proper food labeling and suitable price should be implemented.