BACKGROUND: Functional abdominal pain disorders (FAPDs) are common in young people and are characterized by persistent or recurrent abdominal symptoms without apparent structural or biochemical abnormalities. FAPDs are associated with diminished quality of life, school absence, increased health care use, and comorbid anxiety and depression. Exposure-based internet-delivered cognitive behavioral therapy (ICBT) has demonstrated efficacy in alleviating abdominal symptoms and improving quality of life. However, a deeper understanding of effect mechanisms and identification of possible additional treatment targets could refine treatment. OBJECTIVE: This protocol paper aims to describe a study focusing on children and adolescents undergoing ICBT for FAPDs, aiming to further investigate the underlying mechanisms of effect. METHODS: Children (8-12 years), adolescents (13-17 years) with FAPDs, and their respective parents will be included for 10 weeks for ICBT. First, detailed trajectories of effect are examined through a randomized single-case design study involving 6 children and 6 adolescents (substudy 1). Following this, an open-ended explorative pilot study with 30 children and 30 adolescents explores potential illness-related cognitive biases and interoceptive accuracy before and after treatment (substudy 2). Finally, spanning across these 2 substudies, including all parents from substudies 1 and 2, we will assess parental distress and illness worries before and after treatment, and how these factors impact the treatment adherence and outcomes of the child or adolescent (substudy 3). RESULTS: Recruitment of participants began in June 2022 and is finalized for substudy 1 and ongoing for substudies 2 and 3. Recruitment is expected to be completed by January 2025, with final data collection during April 2025. CONCLUSIONS: The findings have the potential to contribute to the ongoing improvement of specialized psychological treatment for FAPDs in young people. TRIAL REGISTRATION: ClinicalTrials.gov NCT05237882; https://clinicaltrials.gov/study/NCT05237882; ClinicalTrials.gov NCT05486585; https://clinicaltrials.gov/study/NCT05486585; OSF Registries osf.io/c49k7; https://osf.io/c49k7. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/58563.