This research is made to look for a formula of management strategic design at the higher education institution / university level using the strategy focused organization concept. In this research Muhammadiyah University of Yogyakarta is used as a research subject of the strategy focused organization concept. The application of strategic management system in the private sector has been popular. On the other side, conceptually, studies that are related to strategic management system in the public sector (non-profit organization) are still rare especially how to formulate design to support the strategy focused organization in this sector. Because of that reason technically this research also can be usefull to fulfill the rareness of organizing or formulating management strategic design system. System of management strategic design is formulated by researcher through literature and empiric data exploration, which are earned from observation. The results from this research are alternatives of management strategic design for higher education institutions. This management strategic design system is hoped will be useful to improve the quality of higher education institution so it can increase the competitive advantages.