BACKGROUND: The NHS is responsible for approximately 30% of all public sector carbon emissions. The Climate Change Act 2008 introduced legally binding targets to cut emissions of greenhouse gases (GHGs) by at least 80% of the 1990 baseline by 2050. This paper seeks to examine two different strategies for the treatment of gastro-oesophageal reflux disease and their modelled costs and carbon emissions. METHODS: This study uses data from the costs of care of patients in the REFLUX study and NHS England Carbon Emissions Carbon Footprinting Report to model the carbon emissions associated with medical and surgical treatment of gastro-oesophageal reflux disease. The main outcome measures are modelled financial costs and carbon emissions for medical and surgical treatment pathways. RESULTS: There is a high initial cost (financially and carbon emissions) for surgery, however subsequent year-on-year financial spend and carbon emissions are lower in patients who have had surgical treatment such that the total modelled financial cost of surgery is lower in the 14th year and carbon emissions are lower in the 9th year. The model is sensitive to changes in the efficiency of pharmaceutical procurement and surgical failure rate. CONCLUSIONS: The model has demonstrated that in cases of equivalent clinical benefit one pathway may be preferred on the basis of other factors including carbon emissions.