Collaboration or cooperation relationships by applying the principles of collaborative governance are very important carried out by bureaucracies including higher education institutions in order to be able to provide quality educational services. Education become the important aspect in developing community in all the world therefore, every country has their own policy and implementation concerning education program. In Indonesia education classified into various term of management such as State; Private and Institute that have their own goal and capabilities in developing education in Indonesia. One of the Institute is State Islamic Institutes abbreviated as IAIN Purwokerto that become the research object on how education manage referring on Islamic aspect. Through a descriptive qualitative approach, this study tries to look further at the implementation of collaborative governance principles in partner Islamic Boarding School policies at State Islamic Institutes abbreviated as IAIN Purwokerto to improve the quality and competence of Understanding Qur'an Reading and Writing (BTA) as well as Worship Practice Practices (PPI) both of students and its graduates.