Regardless of how laudable the ECOWAS Protocol on free movement of goods and persons seems, it creates a lacuna which has a propensity of national security crisis. This study examines Nigeria’s National Security and the Challenges of the ECOWAS Protocol on Free Movement of Goods and Persons. Primary and secondary sources of materials were utilized. This study established that insurgency in the north east, farmers/herders’ clashes in the north central, militancy in the Niger Delta and other internal security crises in other parts of Nigeria have been fueled by the supply of arms and light weapons by bandits from neighboring countries. Kidnapping, armed robbery, human and drug trafficking and smuggling of food items and other contraband goods have also thrived in Nigeria as a result of activities of criminal elements from the West African sub-region. These are the challenges that are associated with the ECOWAS Protocol on Free Movement of Goods and Persons, thereby posing a threat to Nigeria’s national security.This study therefore, strongly recommends that, the Nigerian government need not only review her migration Acts to curtail movement of certain goods and persons, but also, should conduct an anatomy of inter-agency integration among the border officials to address rampant cases of unhealthy interagency rivalry at the borders. Keywords: Challenges, ECOWAS, Protocol, Regionalism, National and Security..