Celiac disease (CD) is a chronic autoimmune enteropathy triggered by gluten ingestion, with a well-established association with other autoimmune conditions, particularly autoimmune thyroid disease (AITD). Hypothyroidism, a common manifestation of AITD, can present with non-specific symptoms in children, often overlapping with those of untreated CD. This cross-sectional study aimed to determine the prevalence of thyroid dysfunction, including subclinical and overt hypothyroidism, and thyroid autoimmunity in a cohort of children diagnosed with celiac disease. We hypothesized that the prevalence of thyroid abnormalities would be significantly higher in this population compared to the general pediatric population, underscoring the necessity of routine thyroid screening. Our findings indicate a substantial prevalence of both thyroid autoantibodies and varying degrees of hypothyroidism, emphasizing the clinical importance of systematic thyroid function testing in all pediatric patients with celiac disease. Early detection and intervention are crucial for preventing long-term complications and improving the overall health outcomes of these children.