We examined the role of Helicobacter pylori infection as a cause of recurrent abdominal pain (RAP) among Iranian children in a population-based case–control study to determine the association between H. pylori infection and RAP among schoolchildren. A total of 1558 children aged 6–13 years were examined. Children with RAP confirmed by the Apley and Naish criteria were selected; 145 cases were selected for inclusion and were compared with 145 healthy children recruited from the same area. Both groups underwent stool antigen testing. The prevalence of RAP in the children tested was 9.3%. Children with RAP had a higher H. pylori infection rate than the control group (58.6% vs 44.8%) (OR = 1.744; 95% CI 1.095–2.776). There was no significant difference between the RAP symptoms in children with positive stool test, i.e. infected with H. pylori, and those whose tests were negative. We identified H. pylori infection in more than 55% of the case group. Therefore, H. pylori infection can be considered an important factor for RAP in children.