The North-Western Pakistan region (Tribal Areas and Khyber Pakhtunkhwa) has been caught up in militancy, conflict, terrorism, insecurity and instability for more than a decade. Militancy is a serious threat in the way of education and has affected the education governance in North-Western Pakistan. Also, the mental and psychological development of children in FATA and KP has been badly affected due to continuous attacks on educational institutions by militants. These terrorist activities and military operations have caused massive displacement of the local residents to different parts of Pakistan. Furthermore, Education has been overlooked by successive governments in FATA and many areas in KP where literacy rate is critically low. These areas already lag behind other provinces socially and economically. Poor governance, political instability and terrorism have resulted in illiteracy and deprived the students of their basic right to education. This paper underlines the status of education governance by analyzing the impact of militancy and instability on the education. Moreover, the paper is structured to show how these problems can be addressed through a more comprehensive strategy and programs of action by the government of Pakistan.