Nigeria has been the victim of persistent terrorism, mostly by religious militant group’s i.e, Boko Haram and Al-Qaeda. The motives of both the organizations is the implementation of Sharia law in the state and creation of an Islamic administrative structure for the purpose of which both organizations have made an alliances. This study analyzes the emergence of terrorism and subsequent counter terrorism measures taken by the state of Nigeria in response to militant terrorist organizations of Al- Qaeda and Boko haram. Initially it outlines the meaning of terrorism and the various ways in which states adopt counter terrorism measures, then specifying on Al -Qaeda and Boko haram. The origins, mechanism and reasons of these terrorist activities are scrutinized along with the protective and reactionary policies of the government in order to curb these activities and maintain state security. Examining the role of the government, state and external actors in this situation, this study concludes that peace can be achieved in the region through careful negotiations between all the