This research is proposed to describe the thought of KH. Abdurrahman Wahid (Gus Dur) regarding Pesantren, especially the epistemological discourse on its curriculum. In this research, the author uses library research dealing with literature on history and thought of Gus Dur. The result of the study shows that contemporary Pesantren’s structure of knowledge is a dialectical result of two mainstreams in the early Islamic periods, involving humanism and adoption of helenestical tradition in the Middle East after the aggression of Alexandrian Sultanate. According to Gus Dur, pesantren is an institution taking a giant leap in thought a la Helenistic periods without putting aside the Qur’an and Hadits. Epistemologically, the yellow scripture takes a role as universal values in human life for pesantren disciples. The scripture is understood as a chain of Islamic knowledge from the Prophet and the companions. Gus Dur strongly agree with putting religion as the foundation of Pesantren, but secular knowledge must be taken as well in order to develop the pesantren disciples’ self potential.