The study aimed to explore the priorities of authorities and payers related to policy options for pharmaceutical pricing and reimbursement and to understand the rationale of their preferences. Representatives of competent authorities for pharmaceutical pricing and reimbursement and public payers of the 28 EU countries were invited to express their preferences of 16 pharmaceutical policy measures in a web-based questionnaire. Replies of 27 respondents from 22 countries were analysed through a Multi-Criteria Decision Analysis, using an outranking method based on the ELECTRE III algorithm. Follow-up focus groups were held with 47 representatives of authorities and payers from 29 countries. Respondents to the online survey highly prioritised the policy objectives of equitable access to medicines and long-term sustainability of the health care system. They considered a transparent reimbursement process based on clear rules, pharmacoeconomic evaluations, generic substitution, value-based pricing and tendering as most appropriate policy options to achieve intended policy aims. Least preferred policy options were discounts and similar arrangements, differential pricing and external price referencing. However, the latter is a commonly used pricing policy, and discount arrangements have also been increasingly used. Participants of the focus groups highlighted limitations of external price referencing, including over-paying due to referencing to official prices instead of actually paid, confidential discounted prices. Given the lack of perceived alternatives policy-makers continue applying existing tools. At the same time, they are searching for new policy options that should be based on the principles of fairness, solidarity and transparency.