The Joint External Evaluation tool is a World Health Organization-recommended method for evaluating countries' capacities under the International Health Regulations (2005) (IHR). It encompasses a national preparedness assessment process for public health threats and offers a structured framework for planning and implementing effective response measures. A tailored approach is necessary for Nigeria's federated system of government, in which most constitutional requirements for public health and associated issues are decentralized to the state level. The Nigeria Centre for Disease Control and Prevention (NCDC) developed an assessment tool to identify state-level health security gaps and support the development of improvement plans. With input from state and national public health leaders and legal experts, a legislative evaluation was conducted to determine specific IHR activities that could be implemented within the state's legal framework to accelerate the implementation of the Integrated Disease Surveillance and Response strategy and IHR. The resulting assessment instrument was piloted in Kano, Enugu, and Kebbi states, followed by a consensus meeting to identify additional areas for improvement. The revised tool contains 14 technical areas and 35 indicators tailored to implementing improvement plans. By recognizing the unique characteristics of subnational entities and their implications for pandemic preparedness, the tool provides an innovative approach to health security for countries with multilayered governance structures or geographic diversity. Conducting a subnational health security assessment is a crucial step in ensuring preparedness for public health threats and enhancing health security in Nigeria's federated system of government.