Resource allocation under non-emergency conditions is often challenging. Within the context of a Public Health Emergency (PHE), allocation decisions become significantly more difficult as decisions are often necessary on very short timelines, where relevant information (either evidence or information "on the ground") is changing or incomplete, there is significant potential for harm, and resources are scarce, in unpredictable supply, and likely in high demand. An intentional value-based decision-making approach in such circumstances can clarify the values that ought to guide decisions, offering transparency and consistency, among other benefits. We use the example of vaccine allocation during the COVID-19 pandemic to explore value-based decision-making within a PHE context. We describe several core values that are relevant to PHE decision-making and outline their implications for approaches to vaccine allocation. While we focus on vaccine allocation, the values discussed are relevant to other system-level decisions in both emergency and non-emergency situations. Tips for leaders wishing to adopt a value-based approach to decision-making are offered.