This study examines Nigeria’s public health policy and local government responses to the COVID-19 pandemic, focusing on lessons learned for improved governance in future crises. Grounded in Systems Theory, which emphasizes the interdependence of components within a system, the study aims to evaluate the coordination between federal and local governments, assess the capacity and preparedness of local governments, and analyze the impact of resource allocation, healthcare infrastructure, and financial management on local government responses. A qualitative research design was employed, leveraging secondary data such as government reports, scholarly articles, and media sources, with thematic analysis revealing critical insights. Key findings indicate that while some successes were recorded, systemic challenges hindered effective coordination. Resource disparities, weak healthcare infrastructure, and financial mismanagement significantly constrained local governments, particularly in rural areas. Corruption, policy misalignment, and capacity deficits further compounded these issues. However, urban centres like Lagos demonstrated resilience through stronger governance, robust infrastructure, and community-driven approaches. The study concludes that Nigeria’s public health response during the COVID-19 pandemic highlighted both strengths and structural weaknesses, emphasizing the need for systemic reforms. Recommendations include strengthening intergovernmental coordination through standardized frameworks, combating corruption via digital monitoring and audits, and investing in healthcare infrastructure and local government capacity development. This research contributes to knowledge by underscoring the importance of equitable resource allocation, robust healthcare systems, and effective governance, providing actionable insights for addressing future public health crises in Nigeria.