The global COVID-19 pandemic is unprecedented in its scope and impact. While a great deal of research has been directed towards the response in high-income countries, relatively little is known about the way in which decision-makers in low-income and crisis-affected countries have contended with the epidemic. Through use of an a priori decision framework, we aimed to evaluate the process of policy and operational decision-making in relation to the COVID-19 response in Somalia, a chronically fragile country, focusing particularly on the use of information and the role of transparency. We undertook a desk review, observed a number of key decision-making fora and conducted a series of key informant and focus group discussions with a range of decision-makers including state authority, civil society, humanitarian and development actors. We found that nearly all actors struggled to make sense of the scale of the epidemic and form an appropriate response. Decisions made during the early months had a large impact on the course of the epidemic response. Decision-makers relied heavily on international norms and were constrained by a number of factors within the political environment including resource limitations, political contestation and low population adherence to response measures. Important aspects of the response suffered from a transparency deficit and would have benefitted from more inclusive decision-making. Development of decision support tools appropriate for crisis-affected settings that explicitly deal with individual and environmental decision factors could lead to more effective and timely epidemic response.