The functional efficiency of an institution of higher education depends on the size of the available resources and their efficient use, which is expressed using corresponding indicators eg the duration of study. Therefore, there is a need of using new and intelligent models and tools to control and evaluate the educational work. Such models give an emphasis in the processes of developing criteria, techniques, and indicators, and facilitate measurement and performance’s investigation. Recent research showed that Balanced Scorecard gained preferences of the administration of Educational Institutions. This paper presents initially a discussion of basic elements in a balanced target setting in the area of Higher Education and then the basic steps for implementing the balanced scorecard technique for the case of the evaluation of a Greek Higher Education Institute according to the evaluation criteria that are set by the Hellenic Quality Assurance Agency (ADIP).