Higher education institutions in pursuit of excellence have been supported on the application of tools to find continuous improvement in the activities and services that they offer. The Lean Six Sigma model for higher education institutions has become a choice that establishes techniques and tools to improve the quality, efficiency and effectiveness of administrative and academic processes. This article shows the application of the Lean Six Sigma model for Higher Education Institutions in the case study university in the issue process of certificates, where it was identified that one of the problems that occurred most frequently was non-compliance over time average delivery of certificates to the customer. The results of the application made it possible to identify the bottlenecks in the service, which in turn became opportunities for improvement and all this caused: establishing instructions to request the issuance of records certificates, creating an application on the web page to receive electronic payments through a secure and online system, characterize the process in terms of information flow, increase the capacity of the process for high demand for the service, assign a person to verify only for the payment validation stage and digitize the entire academic history of graduates and students.