FGIDs in children and adolescents (ROME III classification) have a significant impact on the daily functioning and quality of life. Often it is the pain that is one of the main contributors to the burden of functional dyspepsia, functional abdominal pain (syndrome), and irritable bowel syndrome. Current knowledge confirms that a number of integrated networks at cortical and subcortical sites are responsible for the experience of pain. From the work of Mayer and Tillisch (2011), mainly based on structural and functional magnetic resonance imaging and positron emission tomography, it has become clear that abdominal pain syndromes are disorders of the bi-directional mind–brain–gut interactions. In this multi-factorial bio-psycho-social model we recognize the importance of neurobiological processes in the mind–brain–gut interactions, leading to alterations in motility, sensation, and immune functions. Medical treatment often offers little or no relief. Until now pharmaceutical research has not succeeded in developing safe new drugs with an effect on the brain–gut axis. More recent published research shows the rationale for the use of medical hypnosis in FGID. In this article the author will illustrate her specific approach in a pediatric gastroenterology clinic with children and adolescents with FGIDs. Being a pediatric gastroenterologist, the author emphasizes the importance of a clear diagnosis, explains the rationale for educating the patient and his or her parents on the multi-factorial bio-psycho-social model and the concepts of chronic pain, discusses the specific settings and pitfalls for hypnosis treatment in children, and last but not least, provides some examples of hypnotic sessions used with FGIDs.