INTRODUCTION: Patients with functional gastrointestinal disorders (FGIDs) have a decreased quality of life (QoL). Psychological illnesses are strongly associated with FGIDs. This study examined the effect of a comprehensive psychological intervention programme designed for refractory FGID patients. METHODS: Refractory FGID patients at a tertiary gastroenterology unit were encouraged to participate in a psychological intervention programme, which included screening for anxiety and depression in patients, educating patients and physicians on FGIDs, and providing early access to psychiatric consultation for patients with significant psychological illnesses. The duration of follow-up was six months. Outcomes were measured using the Irritable Bowel Syndrome-QoL (IBS-QoL) instrument and the EuroQol five dimensions (EQ-5D) questionnaire. RESULTS: A total of 1,189 patients (68% female, 80% Chinese, mean age 48.6 years) participated in the programme. Among these participants, 51% had a significant psychological disorder (Hospital Anxiety and Depression Scale [HADS] anxiety or depression score > 7). These participants had a significantly poorer QoL (IBS-QoL and EQ-5D, both p < 0.0001), and were more likely to be single or English-speaking, as compared to the participants without psychological disorders. Participants who completed ≥ 3 months of follow-up (n = 906) showed significant and durable improvement. High baseline HADS anxiety score predicted improvement (p < 0.001), with participant IBS-QoL and EQ-5D scores decreasing over time. CONCLUSION: The intervention programme was associated with a clinically meaningful improvement in the QoL of patients with refractory FGIDs. High baseline anxiety was predictive of improvement.