The misuse of non-profit organisations (NPOs) for terrorism financing in Indonesia has become a persistent challenge, with both registered and unregistered entities exploited under humanitarian, religious, or educational fronts. Despite legal frameworks such as the 2013 Anti-Terrorism Financing Law, enforcement remains limited, and regulatory oversight is often fragmented. This paper proposes a structured and empirically grounded framework to assess the terrorism financing risk of NPOs in Indonesia using the Analytic Hierarchy Process (AHP). Building on Wardhana’s doctoral research, which identified eight key indicators of high-risk NPOs through qualitative analysis, this study addresses the need for a quantifiable and operational model. The indicators are organised into internal and external dimensions, each assigned fixed weights based on empirical relevance and contextual interpretation. Eleven verified case studies are assessed using this model, generating threat scores that are visualised in a risk matrix to classify each NPO into low, moderate, or high-risk categories. The model enhances consistency in intelligence analysis and regulatory monitoring, offering a practical tool for prioritising oversight and resource allocation. It also provides strategic value for broader adoption by regional and international counter-terrorism frameworks, particularly in jurisdictions where enforcement capabilities are limited and non-profit sector vulnerabilities remain under-addressed.