This dissertation is based on the demand of changes towards boarding school institution, which becomes academic debates about tradition and modernization of boarding school education system by Islamic scholars and thus becomes challenges for boarding schools. This research discussed boarding school education system based on the point of view of KH. Abdurrahman Wahid. This research design by using library research as the instrument with a descriptive analysis of historical approach and pedagogical comparative. The primary source of the data is the work by KH. Abdurrahman Wahid, such as Menggerakkan Tradisi; Esai-Esai Pesantren, BungaRampai Pesantren: Kumpulan KaryaTulis Abdurrahman Wahid, “Pesantren as a subkultur, in M. Dawam Rahardjo (ed), Pesantren dan Perubahan, Islam kosmopolitan, Islamku Islam Anda Islam Kita, as primary sources. This paper concludes that the thinking of KH. Abdurrahman Wahid about boarding school education system is essential in responding to the changes by keep referring to the boarding schools subcultures. It can be seen from some of KH Abdurrahman Wahid's thoughts, such as, first, the aim of boarding school education is dynamic does not only mean to tafaqqu fi al-din, but also to gain knowledge on religious sciences and others. So that students have extensive knowledge, religious knowledge, and general knowledge and skills. Second, the educational program of boarding school education is adaptively by maintaining integrated the curriculum of Islamic sciences and others by simplifying the boarding school curriculum and adjusting it into the development of sciences and technology. Third, the process of boarding school education is innovative by maintaining learning methods sorogan and wetonanthe main characters of boarding school education; however, efforts to the perfect educational system at boarding school must be continually made, especially those related to methods of teaching and implementation of materials in the boarding school. Besides promoting the important findings above, this dissertation recommends to manager and development of boarding school education system to be more competitive, relevant to the needs of society, and able to answer the demands of the times in accordance with the potential and distinctiveness Islamic boarding schools.