The current government in Japan is prioritizing university reform as one of its policies for Japanese revitalization. In fact, university reform is not a new word. Universities have made several reforms since the 1990s. However, a recent government policy has necessitated multidimensional reforms in all functions of education, research, and social service. These requirements include an emphasis on learning outcomes, international 'tuning' of teaching contents, internationalization of universities, establishment of world-class research universities, professionalization of research administration, contribution towards innovation, and further development of innovative talents. This policy calls for connections between higher education policy and science and technology (S&T) policy, but this has not yet been fully achieved. Additionally, a disconnection can be observed between higher education research and S&T policy research. In this special issue, researchers in the higher education, S&T policy, and STS (science technology and society) fields, as well as the Vice-president for Research contribute to the discussion on current issues in Japanese universities.