Functional gastrointestinal disorders (FGIDs), including irritable bowel syndrome (IBS), often show limited response to standard medical treatments, making psychotherapy an important option. Gut-directed hypnotherapy (GDH) has established efficacy, yet treatment-resistant cases remain. We present a case of a woman in her 40s with diarrhea-predominant IBS unresponsive to pharmacotherapy. Initial GDH following the North Carolina Protocol led to partial improvement but persistent anxiety. Stabilization strategies such as the Extended Container Technique and autonomic regulation were introduced, followed by resource development. As traumatic memories appeared relevant, trauma-focused approaches including eye movement desensitization and reprocessing (EMDR) and ego state therapy were integrated. Symptom remission was achieved, with long-term resolution of IBS symptoms despite minor anxiety recurrence after treatment. This case illustrates how combining GDH with trauma-focused psychotherapy may benefit refractory IBS, consistent with evidence linking trauma to FGIDs. However, as evidence is limited, controlled studies are required. Clinically, careful psychoeducation and culturally sensitive introduction of hypnosis are essential in Japan, where negative perceptions of hypnosis persist. This report highlights the need for comprehensive, individualized approaches to psychotherapy for FGIDs.