The 2019 novel coronavirus (COVID-19) pandemic has created unprecedented challenges for policymakers and scientific experts charged with preventing the spread of the virus. In upending the usual mechanisms for political deliberation, the pandemic offers a window into the co-production of governmental policy decisions and scientific evidence. Taking the German state of Bavaria as a case study, this article draws on expert interviews with individuals directly involved in high-level pandemic decision-making to explore the changing relationships between policymakers and scientific experts. The challenges that emerged in the Bavarian context illustrate that while uncertainty has long been understood as constitutive of scientific knowledge, it became a stumbling block for policymakers due to newfound degrees of urgency and implications of decision-making in relation to the pandemic. In order to better address the emergent, evolving problems posed by public health crises, uncertainty must also be understood as formative in the work of policy.