Abstract Background Autoimmune thyroid diseases (ATDs) are heterogeneous group of acquired disorders that are characterized by the presence of circulating anti-thyroid antibodies, infiltration of the thyroid gland by reactive B and T lymphocytes in addition to altered thyroid function. This study aimed to explore the thyroid function profile and H. pylori infection in a sample of pediatric patients with autoimmune thyroid disease. Methods This case control study included 31 pediatric patients diagnosed with ATDs proven by positive thyroid autoantibodies and 31 healthy age and sex matched children were included as control group. Detailed history including clinical manifestations and treatment modalities were taken. Free T4, free T3, TSH, anti-thyroglobulin and anti-tissue peroxidase, H. Pylori stool antigen and thyroid ultrasound were done. None of our included children have received treatment for H. pylori infection. Results Out of the 31 patients, 11 were diagnosed with Graves’ disease (35.48%) while 20 were diagnosed with Hashimoto thyroiditis (64.52%) with mean age of 13.515 ± 3.176 and 14.081 ± 2.715 years respectively. There is no statistically significantly difference in thyroid ultrasound findings in children with GD and HT. H. pylori infection was significantly higher in children with ATDs (51.6%) in comparison to healthy children (25.8%). 17 of the 31 children with ATDs had dyspeptic symptoms with insignificant difference between H. pylori positive and negative children. Regarding treatment modalities, 18 of children with ATDs (58.1%) were controlled on medications while 13 were uncontrolled (41.9%) and needed frequent adjustment of doses or surgical intervention. 19 children with HT (95%) and 7 children with GD (63.6%) received medical treatment only, while 1 patient with HT (5%) and 4 children with GD (36.4%) underwent thyroidectomy after a duration ranged from 3 to 6 years of medical treatment. In Conclusion Hashimoto thyroiditis was the most prevalent ATD in pediatric age group. H. Pylori infection is more frequent in children with ATDs. Medications alone may be insufficient to achieve symptoms control in children with AUTs and surgical intervention may be required. Further studies are required to evaluate the impact of H. pylori infection eradication on thyroid function in children with ATDs.