Congenital hyperinsulinism (CHI) is a rare, genetic disease which causes persistent hypoglycaemia, typically in new-borns. Patients with the diffuse disease variant often require near-total surgical removal of the pancreas, causing insulin-dependent diabetes mellitus (IDDM). The CHI economic burden is currently unknown. This study aimed to estimate the annual cost of illness (COI) of CHI patients in the UK from a service provider perspective (National Health Service, NHS and Personal Social Services), and to explore cost distribution within the patient population. The model was based on standard practice of two CHI centres of excellence. Model inputs were informed by a pragmatic literature review, NHS Reference Costs (2015-2016) and the British National Formulary (2017). Only direct costs to the NHS and Personal Social Services were considered. A prevalence-based approach was used and annual costs incurred at all ages were calculated. A deterministic sensitivity analysis (DSA; run at 10%) identified major cost drivers. The COI of CHI patients to the NHS was £3,408,398.59 annually and average cost per patient was £2124.95. Cost distribution was skewed among CHI patients, with 5.9% of patients (95 patients in their first year of life) contributing to 61.8% (£2,105,491.07) of total costs. DSA results identified lack of response to first-line therapy and IDDM development post surgery (and associated healthcare costs) as major cost drivers. Despite its rare disease status, estimated annual costs of CHI to the NHS were substantial. Development and management of post-surgical IDDM as a major cost driver highlights the need for effective treatments to mitigate such consequences and costs.