The purpose of this study is to explore the model of of organizational culture at Pesantren (Islamic boarding) university, the development of academic culture, and how to anticipate the obstacles, and who is responsible and will be involved in the change and development of the academic culture. Pesantren university is an institution, which organizes higher education programs and is bound by the Laws regulation, to build an academic culture, which is slightly different from pesantren culture. Building an academic culture means creating a new culture within the pesantren envnironment, which focuses on research and development activities, which mainly undertakes documenting the research. Building an academic culture, similar to building an organizational culture, which can be conducted in the following 6 stages; 1) evaluating the organization’s situation and determining strategic objectives and direction; 2) analyzing the existing culture and sketching the desired cultural; 3) analyzing the gap between what is in and what is desired; 4) developing a cultural development plan; 5) implementing the plan; 6) evaluating changes and new efforts to invlove in sustaining cultural change. Steps to build and maintain an academic culture, carried out in the following combination of programs: changes in recruitment and selection procedures; forms socialization and training programs; conducting performance appraisal system; promoting sucessful people in expressing and symbolizing the desired culture; leadership that communicates cultural values in speech, action and material arrangements; the use of academic symbols, in the form of language, action and material objects. The actors of change are the Founders and Leaders, who are assisted by the underlying structure with limited proportions. It is necessary that the appropriate Leadership role to the academic culture, not shifting from the basic values of Pesantren, and open attitude to the development of dynamic academic culture follow the demands of the development of Higher Education.