Children with pain-related functional gastrointestinal disorders (P-FGIDs) have an increased risk for school absenteeism, depression, anxiety and low quality of life. Exposure-based cognitive behavior therapy (CBT) has shown large treatment effects in adults with irritable bowel syndrome, but has not been tested for children 8-12 years with P-FGIDs. The aim of this trial was to test the feasibility, acceptability and potential efficacy of a newly developed exposure-based CBT for children with P-FGIDs. The children (n = 20) with a P-FGID, were referred by their treating physicians. The participants received 10 weekly sessions of exposure-based CBT and were assessed at pre-treatment, post-treatment and 6-month follow-up. Children improved significantly on the primary outcome measure pain intensity at post (Cohen's d = 0.40, p = 0.049) and at 6-month follow-up (Cohen's d = 0.85, p = 0.004). Improvements were also seen in pain frequency, gastrointestinal symptoms, quality of life, depression, anxiety, school absenteeism and somatic symptoms. Improvements were maintained or further increased at 6-month follow-up. The children engaged in the exposures and were satisfied with the treatment. Exposure-based CBT for children with P-FGIDs is feasible, acceptable and potentially efficacious.