Purpose: The study aims to summarise the major Lean tools used in higher education institutions (HEIs) and their impact on different operational performances. Design/methodology/approach: A scoping review was conducted to achieve this objective, systematically identifying and synthesizing relevant literature on Lean tools in HEIs, employing the PRISMA methodology for structured analysis. Journal papers from 2000 - 2024 were reviewed, focusing on peer-reviewed journals indexed in Scopus. The screening process yielded a final set of 23 acceptable studies for further analysis, considering only English-language articles and reviews focused on the adoption of Lean tools in higher education processes and their associated benefits. Findings: Lean tools in HEIs enhance the operational performance by streamlining processes and resulting in improved service quality, increased overall efficiency and effectiveness in both academic and administrative operations. Value stream mapping (VSM) emerges as the most important technique, followed by 5S and Kaizen to foster a culture of continuous improvement. Theoretical implications: The research contributes to the development of theory by providing an understanding of the use of lean tools and principles in the specific sector of higher education institutions and highlighting where the gaps lie in current theory about the use of these same tools in higher education. This prompted us to create new theoretical structures to achieve operational excellence in areas such as office work, academic teaching methods, student support and building maintenance at colleges and universities. Practical implications: The benefits of using Lean tools are not only evident in key performance indicators, but also in areas such as teaching processes and the improvement of administrative processes through knowledge sharing, which enables continuous improvement and a change in the culture of quality education. Originality: The study critically examines and categorize the Lean tools that are most relevant and applicable within the unique context of HEIs. By focusing on this sector, we address a gap in the literature, as Lean implementation has been relatively understudied compared to other methodologies and other sectors (i.e., manufacturing or service industries). To the best of our knowledge, this is the first study to categorize the Lean tools adopted in HEIs, the processes in which they have been implemented, and the benefits derived from their adoption, from an operational excellence perspective.