Lean is a philosophy that is seen as a solution to resolve the problem of efficiency in various industries. It can be used to eliminate all forms of waste in the workplace. The implementation of lean is not only applied in manufacturing but is very important to be applied in other fields, such as in Higher Education Institution. Studies on the topic of lean in the workplace have been carried out, but most of the study has been conducted within a manufacturing context. This study aims to determine the type of waste that is most important to be eliminated first by using the Waste Assessment Model and find the root of the waste problem. This study developed the relationship between waste and find out the effect of waste on each other in Higher Education Institution that focused on teaching and learning process. The steps of this study consist of three-step, such as waste identification, waste assessment, and root cause analysis. From data collection show that there are 46 forms of waste in the teaching and learning process. The results of the Waste Relationship Matrix showed three types of waste must be removed first, namely overproduction, defects, and non-utilized talents. 5-Why’s is used to find out the root causes of waste which is the most important to be eliminated first in the teaching and learning process.