Objectives This study aimed to investigate the association between Helicobacter pylori infection with diabetes mellitus type one and the effect of infected Helicobacter pylori on glycemic control. Methods This case control study was conducted on children with and without type 1 diabetes mellitus (T1DM). Demographic data and gastrointestinal symptoms in both groups and glycemic control status and duration of diabetes were recorded in patients with T1DM. Stool test was done on all children to detect Helicobacter pylori antigen. Results Sixty three children with T1DM with a mean of 10.88 ± 2.84 years and 105 control children with an average age 10.17 ± 2.55 years (P = 0/09) were involved in this study. The frequency of Helicobacter pylori infection in patients with T1DM was 17/ 63 (27%) and 25/105 (23.8%) in control group, (P = 0/64). The frequency of bloating, epigastric pain and nausea was not significantly different between the two groups. The frequency of epigastric pain in children with diabetes with helicobacter infection was significantly higher than non-infected children with diabetes (29.4% vs. 2.2%) (P = 0.004).The mean duration of diabetes (P = 0.53), age diagnosis of diabetes (P = 0.09), fasting blood glucose (P = 0.18), glycosylated hemoglobin (P = 0.08) and the daily insulin dose (P = 0.18) in patients with T1DM with and without helicobacter pylori infection had not significantly different. Conclusions There was no significant association between Helicobacter pylori infection and diabetes in children 5-15 years old, and glycemic control status was not difference in patients with T1DM with and without Helicobacter pylori infection.