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The COVID-19 pandemic has caused significant morbidity and mortality since its emergence in December 2019. In Nigeria, the government inaugurated the Presidential Task Force on COVID-19 to coordinate resources while the Nigeria Centre for Disease Control led the public health response. The Nigeria Ministry of Defence Health Implementation Programme (MODHIP), in partnership with the US Army Medical Research Directorate - Africa/Nigeria, responded immediately to the pandemic by establishing a public health emergency operations center to coordinate the military response in support of national efforts. MODHIP has 5 functional units and 6 pillars that coordinate testing, surveillance, case management, risk communication, logistics, research, and infection prevention and control. It developed an incident action plan and each pillar had its own terms of reference to guide specific response activities while preventing duplication of efforts within the military and the Nigeria Centre for Disease Control. In addition, awareness and sensitization sessions were conducted on preventive practices for COVID-19 and infrastructure was provided for hand hygiene and screening at all military facilities. Military laboratories were configured for SARS-CoV-2 testing while selected military health facilities were equipped and designated as COVID-19 treatment centers. Research proposals aimed at better understanding the disease and controlling it were also developed. The traditional combat role of the military was redirected to complement this public health emergency response. In this article, we highlight gaps, opportunities, and lessons to improve military participation in public health emergency response in the future. More funding and multisectoral collaboration with civilian institutions are key to strengthening military public health emergency preparedness and response capabilities.