Background Functional abdominal pain (FAP) is not only a highly prevalent disease but also poses a considerable burden on children and their families. Untreated, FAP is highly persistent until adulthood, also leading to an increased risk of psychiatric disorders. Intervention studies underscore the efficacy of cognitive behavioral treatment approaches but are limited in terms of sample size, long-term follow-up data, controls and inclusion of psychosocial outcome data. Methods/Design In a multicenter randomized controlled trial, 112 children aged 7 to 12 years who fulfill the Rome III criteria for FAP will be allocated to an established cognitive behavioral training program for children with FAP (n = 56) or to an active control group (focusing on age-appropriate information delivery; n = 56). Randomization occurs centrally, blockwise and is stratified by center. This study is performed in five pediatric gastroenterology outpatient departments. Observer- blind assessments of outcome variables take place four times: pre-, post-, 3- and 12-months post-treatment. Primary outcome is the course of pain intensity and frequency. Secondary endpoints are health-related quality of life, pain- related coping and cognitions, as well as selfefficacy. Discussion This confirmatory randomized controlled clinical trial evaluates the efficacy of a cognitive behavioral intervention for children with FAP. By applying an active control group, time and attention processes can be controlled, and long-term follow-up data over the course of one year can be explored.