Pesantren (Islamic boarding schools) as an educational institution has a clear social base, because its presence together with the community. In essence, the boarding scholl is life of, by, and for the community. This vision needs the role and function of the boarding school which is in line with the condition of the community, nation and the development state. The management leadership in the term of masyayikh council prone to democratic leadership-paternalistic behavior. It is caused by the dominance of power as the part of the masyayikh committee authority given to the board, so that the daily creativity constrained by tradition and culture of pesantren. This study aims to describe the management of leadership behaviour in the Islamic School and identify the organization's management systems and also the management of decision-making in the Islamic School of An-Nuqayah Guluk Guluk at Sumenep Madura. This research is a field study with a qualitative approach of case studies type in boarding school of An-Nuqayah Guluk-Guluk Sumenep Madura. The data collection is done by indepth interviews, as well as through observation and documentation. The data are analyzed in an interactive and comparative konsan. The results of this study are: first, the management of leadership behavior at the school of An-Nuqayah at Guluk Guluk-guluk Sumenep Madura from the first generation, the second, up to this recent generation, has the transformation (change) of leadership style, that is, from the individualism- charismatic to the collective-charismatic , and also from the charismatic-autocratic to the charismaticdemocratic; second, the organization's management systems in schools of An- Nuqayah at Guluk Guluk-guluk changes from the unstructured into the structured one. It changes into the models of the circle spider webs (webbed), that the goal is to tie the whole togetherness and cooperation in running the organization; and third, management decision-making in the school of An- Nuqayah at Guluk Guluk Sumenep Madura has changed from the unprogrammed decision into the Bahtsul Masa'il al- 'amma wa Al-tabayyun.