Background & Aims: Scalable and effective treatments are needed for children with functional abdominal pain disorders (FAPDs). We performed a randomized controlled trial of the efficacy and cost effectiveness of cognitive behavioral therapy delivered online (Internet-CBT) compared with usual therapy. Methods: We studied children (age, 8–12 y) diagnosed with FAPDs, based on the Rome IV criteria, in Sweden from September 2016 through April 2017. The patients were assigned randomly to groups that received 10 weeks of therapist-guided, internet-delivered cognitive behavioral therapy (Internet-CBT, n = 46) or treatment as usual (treatments within the health care and school systems, including medications and visits to doctors and other health care professionals; n = 44). The primary outcome was global child-rated gastrointestinal symptom severity assessed using the Pediatric Quality of Life Gastrointestinal Symptom scale. All outcomes were collected from September 2016 through January 2018. Secondary outcomes included quality of life, gastrointestinal-specific anxiety, avoidance behaviors, and parental responses to children's symptoms. Societal costs and costs for health care consumption were collected during the treatment. Results: Children who received Internet-CBT had a significantly larger improvement in gastrointestinal symptom severity with a medium effect size (Cohen's d = 0.46; 95% CI, 0.05–0.88; number needed to treat, 3.8) compared with children who received the treatment as usual. The children's quality of life, gastrointestinal-specific anxiety, avoidance behaviors, and parental responses to children's symptoms also improved significantly in the Internet-CBT group compared with the treatment as usual group. The effects of Internet-CBT persisted through 36 weeks of follow-up evaluation. Children who received Internet-CBT had significantly less health care use than children who received treatment as usual, with an average cost difference of US $137 (P = .011). We calculated a cost savings of US $1050 for every child treated with Internet-CBT compared with treatment as usual. Conclusions: In a randomized trial of pediatric patients with FAPDs, we found Internet-CBT to be clinically cost effective compared with treatment as usual. Internet-CBT has the potential to increase the availability of treatment for a number of patients and reduce health care costs. ClinicalTrials.gov: NCT02873078.