Background: The coronavirus disease (COVID) pandemic exposed and exacerbated vulnerabilities within rural public health systems across the United States. Rural communities faced unique challenges, including lower vaccination rates, persistent misinformation, resource inadequacies, and heightened political polarization. Public health officials in rural Wisconsin played a critical role in the pandemic response, often as the primary or sole source of public health information and services for local residents. This study examines the challenges faced by rural public health officials during the pandemic and the strategies they employed to mitigate the spread of COVID and promote vaccine uptake. Methods: This qualitative study employed semi-structured interviews with 14 public health officials from 12 rural counties in Wisconsin, purposefully selected from counties with the highest and lowest COVID mortality rates. Interviews explored officials’ experiences with pandemic response, vaccine distribution, community engagement, and barriers to public health implementation. Thematic analysis was conducted using an inductive coding approach to identify key themes related to public health challenges and response strategies. Results: The following core themes were identified from public health interviews: (I) rural public health officials encountered numerous challenges for COVID mitigation further complicated by long-standing inadequacies in the rural health system; (II) effective strategies for mitigating COVID engaged community members, quickly adapted to changes, and effectively navigated misinformation and political polarization of COVID; and (III) public health officials managed with the available resources and relied on community strengths to best mitigate the impact of the pandemic. Conclusions: Rural public health officials played a vital role in combating misinformation, adapting communication strategies, and promoting vaccine uptake, often with limited resources and significant resistance. Strengthening rural public health infrastructure, ensuring long-term flexible funding, and fostering community trust are critical to improving pandemic preparedness and future public health interventions. The findings provide actionable recommendations for policymakers, public health practitioners, and researchers focused on enhancing rural health resilience in the face of emerging public health threats.