Sustainability of the environment is affected by various organizations’ environmental performances, such as Higher Education Institutions (HEI). The HEI’s environmental performances are divided into different categories, such as energy, water, waste, mobile sources, paper, food, and built-up area. Implementation of Environmental Management System (EMS), such as ISO 14001:2015 has been acknowledged to improve HEI’s environmental performances. Despite that fact, only a few HEI that implemented ISO 14001:2015 for their EMS in Indonesia. This article analyzes potential barriers to implementing EMS in Indonesian HEI based on a systematic literature review and in-depth interviews at the case university. There are 25 potential barriers found, analyzed, and then summarized. Five main potential barriers are identified: (1) lack of commitment from the management of the stakeholders; (2) lack of financial resources; (3) lack of expertise on EMS; (4) organizational; (5) lack of engagement from student, staff, and faculty. The study’s results can be used as additional consideration for HEI to overcome barriers in implementing EMS.