Discussion of how to ensure the efficient use of resources and maximize the contribution made to society by higher education institutions is growing in importance. In response, this research uses Data Envelopment Analysis (DEA) to measure the technical efficiency of academic Units in a Chilean university. A methodological framework was developed that was adapted to the availability of information and productive technologies by applying procedures that allow for the reduction of variables to an appropriate quantity to ensure the reliability of the DEA results and to ensure that the boundary conditions enable the objectives of the university as a whole to be addressed and not just those of the Academic Units. Courses of action are also proposed to improve efficiency. Subsequently, the results are compared with the academic evaluation mechanisms currently used by the university. The conclusions identify a discordance between the results and identify the modifications the university should make to its evaluation tools in order to improve their efficiency. These results are applicable to other Chilean and Latin American higher education institutions.