This research is about anti-terrorism cooperation between the National Agency for Counterterrorism (Badan Nasional Penanggulangan Terorisme/BNPT) and civil society, study case Muhammadiyah disengagement in the signing of Memorandum Of Understanding between BNPT and Islamic organizations in 2011. The theory applies are Terrorism, Security sector reform and Cooperation. As civil society, Muhammadiyah has conducted anti-terrorism efforts through its structural and cultural roles in politic, socio-economic, diplomatic and education aspect. Unfortunately, there has not been any framework of cooperation established between Muhammadiyah and BNPT, due to several hindering factors. Firstly, Muhammadiyah and BNPT have different perspective in addressing issues on terrorism and anti terrorism methodology. Secondly, political conflict. Thirdly, BNPT?s constraints in time, human resources and funding. Forthly, lack of BNPT?s political will. Actually, Muhammadiyah possess ideological and organisational potential that may facilitate the dissemination of anti terrorism more effective and efficient. Therefore, this study recommends the need for BNPT and Muhammadiyah to strengthen organisational commitment and to start building communication. In addition, the concept of deradicalization applied by BNPT needs to be evaluated and developed. This study is a qualitative research and using descriptive analysis method.