This study investigates how principals exercise leadership to tackle the difficulties faced by Islamic Senior high schools or Madrasah Aliyahs of three areas in Indonesia: Western, Central and Eastern Indonesia. Employing qualitative methods, the researchers applied multiple case studies technique. The information gathered originated from separate case study classrooms, purposefully chosen madrasah Aliyahs/ Islamic-based high school from government, private, challenging and high-performing schools. It has been disclosed that madrasahs experience countless difficulties, including leadership, curriculum development, classroom equipment, financing and teacher efficiency. In the west and center of Indonesia, madrasahs mainly hampered by the poor infrastructure, learning facilities and lack of financial support, while in the east part beside the financial issues, teachers' performance become huge concerns.The madrasah managers, senior institutional officials, have a critical part to perform in solving these issues, in particular by developing teaching and learning procedures and improving the value of education and the enhancement of schooling. The study found that a kinship leadership is strongly indicated to the principal leadership behaviour. A culture embedded, leadership education, and experience gained by the leaders provide a deep insight on the way they lead an organisation. Although some madrasah adapted professional system like in the case of some high performing schools, the kinship and partnership are strongly occupied by the leaders in order to develop their communication and interaction among the members