The system of administering Islamic education with Dutch colonial education during the colonial period has inspired a number of thinkers and organizers of Islamic education to make reform efforts. Their admiration for the success of the colonial school education system in delivering the progress of life, has influenced their decision to adopt the system in the implementation of Islamic education with a slight modification of the curriculum, namely by including Islamic Religious Education material in it. The first Islamic education system in Indonesia is Surau in Minangkabau, Meunasah, Dayah, Rangkang in Aceh and Islamic boarding school in Java. Changes in the administration system in Indonesia occurred significantly, namely after Indonesia's independence, they began to adapt to the school education system, but they still consistently referred to the experience of Islamic history to maintain the purity of the Islamic education system, so they chose to establish Madrasah educational institutions. The system of administering Islamic education by analyzing the historical development of the early establishment of madrasas in Indonesia, after going through the stages of struggle and the development of national education politics, has become a system of administering Islamic education in which the existence of madrasas increasingly shows its strength as an educational institution rooted in traditional Islamic societies. Madrasas grow and develop in various ways, leading to a process of integration in the national and international education systems. Keyword: Islamic Education System in Indonesia