This study aims to quantify and compare preferences of citizens from different European countries for vaccination programme characteristics during pandemics, caused by pathogens which are transmitted through respiratory droplets. Internet panel members, nationally representative based on age, sex, educational level and region, of four European Union Member States (Netherlands, Poland, Spain, and Sweden, n = 2,068) completed an online discrete choice experiment. These countries, from different geographical areas of Europe, were chosen because of the availability of high-quality Internet panels and because of the cooperation between members of the project entitled Effective Communication in Outbreak Management: development of an evidence-based tool for Europe (ECOM). Data were analysed using panel latent class regression models. In the case of a severe pandemic scenario, vaccine effectiveness was the most important characteristic determining vaccination preference in all countries, followed by the body that advises on vaccination. In Sweden, the advice of family and/or friends and the advice of physicians strongly affected vaccine preferences, in contrast to Poland and Spain, where the advice of (international) health authorities was more decisive. Irrespective of pandemic scenario or vaccination programme characteristics, the predicted vaccination uptakes were lowest in Sweden, and highest in Poland. To increase vaccination uptake during future pandemics, the responsible authorities should align with other important stakeholders in the country and communicate in a coordinated manner.