The existence of madrasah in Indonesia in genealogy can be considered as a process of institutional transformation of the traditional Islamic educational system (Surau) and islamic boarding school (Pesantren) system. Madrasah as a modern institution of Islamic education holds the function of Tafaqquh fii al-diin that is expected to provide integral and comprehensive education services. But in its development, there are many constraints faced that caused many criticism to the madrasah education system. Some peoples think that madrasah was disoriented, and some others say there is concept opaqueness of education in madrasah. Madrasah was constrained by dichotomous science stigma, general and religion, which finally broke the focus of madrasah, Such problems must be overcome by establishing a clear concept of integralisasi science, were able to remove the dichotomy that has been rooted in the perception of educational actors. so the philosophical study refers to the basic values which are the basis of all aspects of the Islamic religion is absolutely necessary, in order to establish the concept of Islamic education that is able to realize its function as an institution of Tafaqquh fii al-deen.