The COVID-19 pandemic exposed a multitude of vulnerabilities in Switzerland’s decentralized healthcare system and highlighted the urgent need to strengthen Switzerland’s capacity to respond to health crises and disease outbreaks. In this article, we draw on three distinct areas of analysis of the current functioning of the Swiss healthcare system to examine its strengths and weaknesses, which can serve as a basis for future considerations and strategic priorities. First, we analyze the different levels of nine non-pharmaceutical interventions (NPIs), as defined by the ETH KOF Stringency Index and implemented in the Swiss cantons of Zurich, Vaud, and Ticino, compared with the rate of positive COVID-19 cases, hospitalizations, and deaths. We find that there was no strong correlation between the severity of the nine non-pharmaceutical interventions implemented and lower rates of positive COVID-19 cases, hospitalizations, and deaths. Second, we examine the challenges of Switzerland’s decentralized healthcare system through a literature review and with empirical data obtained from semi-structured interviews with health professionals in Switzerland. We conclude our analysis with the role of central authorities during the COVID-19 pandemic. The results demonstrate that during a national emergency in Switzerland, taking into account other factors that influence the success of a pandemic strategy, there is an opportunity for a more unified, centralized response to reduce the social and economic toll of the pandemic without necessarily risking greater health damage. We recommend that the Swiss federal government use a combination of decentralized and centralized public health and policy approaches and promote greater private–public collaboration with direct communication channels among policymakers, public health stakeholders, and the public to improve pandemic preparedness and response.