This study examined and analysed the relationship between the cost-effectiveness and outcome of radiotherapy for oesophageal cancer among hospitals with varying accreditation levels. We selected 428 oesophageal cancer patients from medical and non-medical centres using the National Health Insurance Research Database, which is maintained by the Taiwanese National Health Research Institutes, and compared their medical expenditure and the outcome of their radiotherapy treatment. In this study cohort of patients with oesophageal cancer, 278 patients were treated in medical centres (mean age: 60.1 years) and 150 patients were treated in non-medical centres (mean age: 62.0 years, P = 0.16). The medical centre group exhibited significantly lower medical expenses, mortality and risk of death compared with the non-medical centre group (adjusted hazard ratio = 1.38, 95% confidence interval = 1.11-1.71). Our study determined that radiotherapy for oesophageal cancer costs significantly less, and medical centres had lower mortality rates than non-medical centres. These findings could provide professional organisations and healthcare policy makers with essential information for allocation of resources.