Because of the comprehensiveness and urgency of environmental challenges, every stakeholder needs to be engaged in reducing environmental impacts. The healthcare sector has rarely been studied, despite its intense effects on the environment, particularly through generating various forms of hazardous waste and intensively consuming energy and water. Many healthcare facilities exist in South Korea, and every citizen frequently visits hospitals thanks to the convenient system. To reduce the environmental impacts of the healthcare sector, the South Korean government has implemented various policy measures aimed at promoting environmental management in that sector. This study evaluated the eco-efficiencies of 21 hospitals from 2012 to 2015 using data envelopment assessment (DEA), used the analytical hierarchy process (AHP) to analyze hospital staff members’ answers to a questionnaire asking about the relative importance and performance of individual environmental management tasks, and also identified environmental management tasks that should be prioritized by building an importance-performance analysis (IPA) matrix using those questionnaire responses. This study found that eco-efficiencies have improved during the period, and that mandatory policy measures were more effective than voluntary agreements for improving eco-efficiency. This implies that rigorous reporting and monitoring should be implemented along with any voluntary agreement. In addition, this study found that the top priorities are “establishment of vision and strategy for environmental management” and “organization of task team for environmental management and task assignment”. This shows the necessity of additional policy measures, such as training or consulting to promote the priorities. In addition to policy recommendations for diffusing environmental management in the South Korean healthcare sector, the methodological approach sheds light for researchers interested in environmental management in the healthcare sector because previous studies depended on qualitative approaches, particularly case studies.