Background and Objective: Helicobacter pylori (HP) is a very common human infection worldwide, colonizing the stomach of 50% of the world’s population. H. pylori play a major role in the development of iron deficiency, chronic gastritis, peptic ulcer and gastric cancer. H. pylori infection is more prevalent in developing countries and its acquisition is predominant in childhood. The aim was to determine the prevalence of HP and its association with serum iron levels in children aged 1-12 years attending the Buea Regional Hospital. Methods: This was a hospital based cross sectional study involving 189 children. About 2 mL venous blood was collected and analyzed using immunoassay diaspot one step H. pylori Test Device and spectrophotometers to determine H. pylori immunoglobulin G and serum iron level respectively. Chi-square and Odd ratio test were used to determine the association at 95% confidence interval. Results: A prevalence of 31.7% (60/189) and 47.1% (73/155) for H. pylori and low serum iron level was observed respectively. There was significantly associated between H. pylori and serum iron levels, with majority (60% (36/60)) of the HP positive participants having normal iron level 60% (36/60) (P=0.007 χ2=9.91). A significant association was also observed between HP and Anemia, with majority (41.67% (25/60)) of those positive for HP experienced mild anemia (P=0.009 χ2=11.55). H. pylori was more prevalent among males 38.04% (35/92) compared to 25.77% (25/97) for females. Conclusion: This study recorded 31.7% and 47.1% prevalence of H. pylori and low serum iron level respectively, in the studied population. Male gender was most likely to be infected with H. pylori infection and children of age group 5 ≤ - < 9 years recorded the highest HP infection. There was significantly associated between H. pylori and serum iron levels, as well as H. pylori and type of anemia, although majority of H. pylori positive individuals had high serum iron level and mild anemia. This may imply that HP remains one of many risk factors or comorbidities of anemia and abnormal iron levels.