Economic evaluations aim to compare the costs and the results of health strategies to guide the public decision-making process. Cost estimation is, thus, a cornerstone of this approach. At present, few national evaluation agencies recommend incorporating the cost of greenhouse gas (GHG) emissions from healthcare actions into the calculation of healthcare costs. Our main goal is to describe and discuss the methodology for integrating the cost of GHG emissions into the field of applied economic evaluations. To estimate this cost, three steps are required: (1) identifying and quantifying the physical flows linked to the production and management of the outputs of healthcare interventions, (2) estimating the quantity of GHG that can be attributed to each physical flow, and (3) valuing these GHG emissions in monetary terms. Integrating the cost of GHG emissions into the calculation of the costs of healthcare interventions is both useful and relevant from a perspective of collective intergenerational well-being. This approach has been made possible thanks to the existence of accounting and monetary valuation methods for emissions. Agencies specialized in health economic evaluations could take up this issue to resolve ongoing questions, thus providing researchers with a methodological framework and public decision-makers with some key insights.