High education based on Islamic boarding house (pesantren) can be an alternative for educational development. As the oldest educational institution in Indonesia, Islamic boarding schools are the basis for the development of education, including the development of higher education. Pesantren was considered very successful in developing the mission of character education. So it was necessary to examine in more depth how government policies are related to the pesantren-based higher education model. University of Ibrahimy Sukorejo, Situbondo is one of the models of a pesantren-based university. A case study with a qualitative approach was used to discuss this research. The results showed that the management of pesantren-based university must apply the principles of accountable management. This means that all parties involved must play an active role, and do not carry personal interests. The holders of power, especially the kyai as managers and controllers must also understand the governance of higher education