The Indonesian Armed Forces used to be at the forefront of the countryʼs counterterrorism efforts. Following the countryʼs democratic transition in 1998, the Indonesian National Police took up the lead role. However, many analysts argue that the military is trying to regain its past dominance in counterterrorism. Regardless of this concern, the military does not have to be at the forefront of the countryʼs counterterrorism efforts to influence the overall policy and practices. The lingering militaryʼs historical legacies remains intact in Indonesiaʼs counterterrorism governance. This research highlights three dynamics: (1) The interagency rivalries; (2) the framing of issues; and, (3) the inherent militaryʼs ideological legacies. Despite various political changes that Indonesia underwent in the past few decades, thesedynamics are still relevant in discussing the contemporary counterterrorism governance and practices in Indonesia. This research will demonstrate the importance of historical understanding to analyse Indonesiaʼs counterterrorism governance.