We evaluated the effectiveness of a synbiotic in the treatment of childhood functional abdominal pain (FAP). Probiotics are effective in the treatment of functional gastrointestinal disorders in adult patients, but there is lack of information in children. Children with FAP, based on the Rome III criteria (n = 115, aged 6-18 years), were randomized to receive either synbiotic (Bacillus coagulans, Unique IS-2, 150 million spore plus FOS, 100 mg) twice daily or placebo for four weeks. Treatment response was defined as ≥ 2-point reduction in the 6-point self-rated pain scale or "no pain". Physician-rated global severity and improvement were also evaluated. Patients were followed for a total of 12 weeks. Eighty-eight patients completed the trial (45 with synbiotic). Response rate was higher with synbiotic than placebo after medication (60% vs. 39.5%, P = 0.044), but was not different between the two groups at week 12 (64.4% vs. 53.4%, P = 0.204). Difference between the two groups regarding the physician-rated global severity over the study period was not statistically significant (z = -1.87, P = 0.062). There was no significant difference between the two groups in physician-rated global improvement (week 4, P = 0.437; week 12, P = 0.111). Receiving synbiotic (OR 2.608, 95% CI: 1.01-6.68) and baseline pain score (OR 2.21, 95% CI: 1.19-4.10) were predictors of treatment response after medication. The synbiotic containing Bacillus coagulans and FOS seems to be effective in the treatment of childhood FAP. Further trials are recommended in this regard.