The Literature on Performance Measurement Systems (PMS) is vast, however, little is found on the design stage of these for Higher Education. The purpose of this article is to present an SMD built for a Biotechnology Graduate Program (GP) to evaluate its performance. The Value Focused Thinking (VFT) approach was used to identify performance criteria. Mathematical modeling technique was used to identify the weights of these criteria through the Decision Support Method with Multiple Criteria: Analytic Network Process (ANP). Stakeholder decision compatibility was tested. Thirty-five performance indicators were built and grouped into eight fundamental objectives. The evaluation of the program identified that its strengths were Percentage of deadline fulfillment (by students) and Percentage of joint orientations between teachers and that managers should prioritize Percentage of patents or products students / teachers and Percentage teachers / students who participated as advisor / consultant.