This study examines the application of system thinking to mitigating terrorism and counter-terrorism in public secondary schools in North Central Nigeria. Drawing upon systems theory and contemporary security literature, the study conceptualizes schools as complex, interdependent systems in which multiple factors—including leadership, policy, technology, community relations, and stakeholder engagement—interact to shape vulnerability to terrorist attacks and the capacity for effective counter-terrorism responses. Employing a descriptive survey research design, the study draws on existing policy documents, national security reports, and empirical literature from Nigeria. A sample of 384 educational administrators, security personnel, and policy analysts was selected through purposive sampling based on their expertise in school security management. The research instrument demonstrated strong validity (0.81) and reliability (0.79), confirming its accuracy and consistency. Data were analyzed using mean and standard deviation for answering research questions, with a 2.50 benchmark on a four-point Likert scale. Hypotheses were tested using chi-square to evaluate relationships between system thinking application and counter-terrorism effectiveness. The findings indicate significant gaps in the application of system thinking to counter-terrorism, with fragmented security responses, inadequate community engagement, and limited technology integration. The study concludes that sustainable counter-terrorism in schools requires strategic governance, systemic coordination, community engagement, and the integration of technology guided by systems thinking principles. Recommendations include the establishment of multi-stakeholder school security committees, the integration of security education into the curriculum, and the development of community-based early warning systems.