Waste in HEIs is difficult to identify, so identifying and prioritizing waste is challenging. This research aims to develop a framework within which to identify and prioritize waste reduction in HEIs. The novelty of this study is that it analyzes and prioritizes waste in HEI from the perspective of four stakeholders in teaching, research, and community services, as well as supporting activities. The process of waste identification was undertaken via observation and literature review, while prioritization of waste was based on the criticality level of waste (CLoW). Determining the criticality level of waste (CLoW) consists of two stages: the first stage is calculating waste scores using questionnaires from students, lecturers, and education staff; the second stage is calculating the critical level of waste using a questionnaire from HEI leaders and analyzing it with fuzzy methods. This study identified 59 types of waste and grouped them into eight types: over-production, over-processing, waiting, motion, transportation, inventory, defects, and underutilization talent. Waste occurs in three HEI activities: teaching, research, community service, and supporting activities. The results also show the priority order of waste reduction and proposed improvements to reduce waste. This study offers a practical contribution to the management of HEIs to identify and prioritize waste reduction. The theoretical contribution of this study is that it fills the research gap of waste reduction prioritization in all aspects of HEI activities involving all HEI stakeholders involved in the business process, namely, students, academics, non-academic staff, and HEI leaders.