Violent extremism is an asymmetric threat that can have an impact on the country’s defense in Indonesia. The Strategy of the National Counterterrorism Agency is one of the efforts to prevent the problem. The purpose of this study is to analyze the strategy of the National Counterterrorism Agency in preventing the threat of violent extremism as well as its synergy with ministries and institutions in Indonesia. The method used in this study is a qualitative method by deepening from various sources on the national action plan to prevent violent extremism by the National Counterterrorism Agency. The theories used are the concept theory of state defense, synergy theory, theory of violent extremism. The results of this study show that acts of violent extremism in Indonesia have threatened the integrity of the nation and state so that it requires handling from BNPT as a body that conducts implementation in counter-terrorism. The purpose of the National Counterterrorism Agency (BNPT) in implementing the national action plan is to improve the protection of the right to the security of citizens. Furthermore, the Joint Secretariat was formed as a means to carry out action to prevent violent extremism through cooperation with ministries, institutions, and local governments. Synergy conducted by BNPT with the Ministry of Religious Affairs (Kemenag) through grounding religious moderation on social media, providing training to Islamic Extension (PAI) and supporting deradicalization programs.