This study uses the “Complete Decomposition” technique to examine the intensity of CO2 emissions in the health sector in Portugal over the period 1997–2014. Our results suggest that improvements in emission intensity in the health sector depend on the design of incentives of replacing fossil fuels with fuels from renewable energy sources and adopting measures to save energy. In addition, capital investment may also contribute to the reduction of the emission intensity in the sector, if the investment is applied to the acquisition of more efficient equipment. We identify areas for action and recommend that public and private sector health professionals should elevate energy efficiency to a top priority. Our results also highlight the importance of the Kyoto protocol.