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Terrorists need money to fund their actions. Financing terrorism in the last two decades has become more complicated worldwide due to the involvement of individuals and networks, partly by misusing religious charity. This study seeks to raise their modus, government countermeasures and challenges in Indonesia. It used terrorist financing theories and a qualitative approach with multi-data collection methods. It found that in the last two decades, terrorist groups in Indonesia, including Jemaah Islamiyah (JI), Jemaah Ansharu Daulah (JAD), and Jemaah Ansharu Khilafah have misused Islamic charities for terrorism actions, including training, falsifying data, purchasing weapons and explosive material, and travelling to conflicting zones. They capitalized on Islamic narratives to cover their terror mission. The Indonesian government has taken strategies and measures to address terrorism financing, such as ratifying international regulations, making follow-up regulations, establishing taskforce and enforcing the laws, covering investigating leaders, arresting the suspecting leaders and freezing the organizations. However, government efforts still pose several challenges in terms of the sensitivity of the issue, the problems in finding proof, inadequate regulation, poor prevention measures and poor law enforcement in the social media.