Recurrent headaches are a frequent problem among children and adolescents. To avoid further aggravation and prevent chronification, it is recommended to inform them about how to adequately deal with or even prevent headaches. Therefore, we designed an educational website informing children and adolescents about the two most common types of primary headaches in this age group: tension-type headache and migraine. In a cluster randomised controlled trial N = 793 5th and 6th graders of six secondary schools received an in-school online-based headache intervention where they explored a website on headache using an accompanying workbook. The study comprised four assessments every four weeks. Half of the randomly assigned classes received the intervention after baseline (intervention group), the other half after the last assessment (control group). Differences in headache-specific knowledge and headache characteristics were analysed with multi-level models. This study supports the use of educational interventions informing about headaches in schools. With this intervention, schoolchildren are given ways to deal with headaches on their own and tools to possibly prevent them altogether.