The aim of this paper is to compare the characteristics of governance in private universities in Japan and Korea. The Private School Act in both countries is analyzed. The Act aims to achieve a reasonable balance between the private university’s need for autonomy (independence) and the public nature of its function. The two countries represent different approaches to guaranting these two principles. Compared to Korea, the autonomy of private university is guaranteed in Japan. In order to assure the autonomy of the private university, the limits of governmental control and the voluntary reciprocal control among private universities are important in Japan. The way to ensure the public nature of the private university also differs between Japan and Korea. In order to enhance the public nature, transparency, and democratization of management of the private university, both counties amended the Private School Act in the mid-2000s. Japan, expanded the external trustees of the university while Korea expanded faculties’ (academics) participation in management.