Switzerland, a wealthy country, has a cutting-edge healthcare system, yet per capita, it emits over one ton of CO2, ranking among the world’s most polluting healthcare systems. To estimate the carbon footprint of the healthcare system of Geneva’s canton, we collected raw data on the activities of its stakeholders. Our analysis shows that when excluding medicines and medical devices, hospitals are the main greenhouse gas emitter by far, accounting for 48% of the healthcare system’s emission, followed by nursing homes (20%), private practice (18%), medical analysis laboratories (7%), dispensing pharmacies (4%), the homecare institution (3%), and the ambulance services (<1%). The most prominent emission items globally are medicines and medical devices by far, accounting for 59%, followed by building operation (19%), transport (11%), and catering (4%), among others. To actively reduce Geneva’s healthcare carbon emissions, we propose direct and indirect measures, either with an immediate impact or implementing systemic changes concerning medicine prescription, building heating and cooling, low-carbon means of transport, less meaty diets, and health prevention. This study, the first of its kind in Switzerland, deciphers where most of the greenhouse gas emissions arise and proposes action levers to pave the way for ambitious emission reduction policies. We also invite health authorities to engage pharmaceutical and medical suppliers in addressing their own responsibilities, notably through the adaptation of procurement processes and requirements.