OBJECTIVES: Gut-directed hypnotherapy (HT) is effective for irritable bowel syndrome (IBS) and functional abdominal pain (syndrome) (FAP(S)) in children. We assessed the cost-utility and cost-effectiveness of HT by self-exercises at home using a compact disc (CD) against individual HT performed by a qualified hypnotherapist (iHT). METHODS: Alongside a multicentre non-inferiority randomized controlled trial among children with IBS and FAP(S) data on treatment response, quality of life (Health Utility Index 3) and societal and health care costs were gathered at baseline (T0), end of  treatment (T1) and 6 (T2) and 12 (T3) months thereafter. Incremental cost-effectiveness ratios with the extra costs per responder and per QALY were estimated and the cost-effectiveness acceptability of CD was assessed for various levels of willingness to pay (WTP) following non-parametric bootstrapping. RESULTS: After one year, CD treatment resulted in cost savings of €397 (95% bca CI: -€794 to -€26; P=0.038) compared to iHT. Treatment response in the CD group (62.1%) was non-inferior to the iHT group (71.1%).  Offering CD treatment instead of iHT treatment saves €4,411  per treatment non-responder. After correction for differences in health utility at baseline, the mean difference in QALYs (0.014 (95% bca CI: -0.032 to 0.060) slightly favoured  CD treatment.  The probability that CD treatment is both, cost saving and gaining QALYs, equals 69.7%; the probability that CD is cost-effective equals 0.825 at a reasonable WTP in children of €50,000. CONCLUSIONS: Home-based treatment with HT exercises on CD for children with IBS or FAP(S) is non-inferior and seems cost-effective compared to individual HT with a qualified therapist and could therefore be offered as first line treatment.