Uganda has faced numerous epidemics over recent decades, necessitating robust health systems to mitigate their impacts. A qualitative approach involving interviews with healthcare professionals and epidemiologists, supplemented by secondary data analysis of official health records. Health systems showed significant variability in their capacity to respond to different epidemic threats, ranging from an effective measles vaccination campaign (78% coverage) to a less successful response to Ebola virus disease (10% case fatality rate). Ugandan health systems exhibited resilience in some areas but vulnerabilities in others, particularly during the Ebola outbreak. Enhance preparedness for emerging diseases by integrating international support and strengthening surveillance networks.