This article explores the effectiveness of a newly developed Pain Neuroscience Education program for children (PNE4Kids) with functional abdominal pain disorder (FAPD). Children (6–12 years) with FAPD were randomly assigned to 1) the experimental group (n = 14), participating in one hypnotherapy session (i.e., usual care) and one additional PNE4Kids session, or 2) the control group (n = 14), participating in two hypnotherapy sessions. Parental pain catastrophizing, the child’s functional disability (parental-proxy), pain-related fear (parent-proxy) and pain intensity, were assessed at baseline and one and three weeks after each therapy session. Pressure algometry and a conditioned pain modulation paradigm were performed at baseline and three weeks after completion of the last therapy session. Parents from both the experimental as well as the control group showed significantly less parental pain catastrophizing (p < 0.01). Children showed significantly less functional disability (p < 0.05), pain-related fear (p < 0.01) and local pressure pain sensitivity (p < 0.05) at short-term follow-up (three weeks after last intervention) in both groups. No significant (p > 0.05) between-group differences were found. Hypnotherapy combined with PNE4Kids did not result in better clinical outcomes compared to hypnotherapy alone. Study limitations include the application of one single PNE4Kids session and the short follow-up time.