The paper presents a methodology for measuring innovation competitiveness of universities stepping on the applied educational innovations within all university functions. The purpose of presenting the methodology is its possible repetitive application in many other than the currently undertaken research for achieving better validation of the necessary steps for measuring Innovation competitiveness of universities. An assumption in the study is that a university may implement, develop and educate innovations only after its ability to manage and implement them into its own organization. A second assumption is that implementing educational innovation in all university functions is the only way to improve university education. Since educational innovations are a highly dynamic and developing field, also dependent from many factors as cultural, political, financial, human and even religious aspects, the currently presented methodology describes how the process of measuring innovation competitiveness of universities may be achieved for a specific scope. The process of measuring innovation competitiveness of universities goes through all stages from first defining the attributes of educational innovation types involved, exploring rankings for university competitiveness and realization of a survey across the scoped for researching universities.