To enhance preparedness for diverse pandemic situations we aim to predict the performance of various pharmaceutical intervention strategies. We gathered domain experts and ran a series of decision conferences where a scenario-based multi-criteria decision analysis (MCDA) model was interactively defined and implemented. Assuming an influenza pandemic, a micro simulation model was used to estimate societal health impact, a health-economic model was used to estimate economic losses, and expert preferences were elicited to define trade-offs between multiple criteria and synthesize various estimates. Sensitivity analysis to address various forms of uncertainty was also conducted. Nine intervention strategies, including the baseline “no interventions” strategy, were evaluated and ranked under five pandemic scenarios for Sweden's population. We conclude that a scenario-based MCDA approach relying on multiple models for assessment of consequences is instrumental in defining robust interventions and support decision-making at the pre-pandemic and pandemic situations.