Abstract Issue This policy research addresses the issue of rare cancers in the European Union (EU). Rare cancers have an annual incidence rate of less than 6/100 000 and face challenges in diagnosis, clinical care, and research investment. Survival rates for rare cancers are lower compared to common cancer types, with significant variations among EU Member States. Description of the problem Policy frameworks for rare cancers are often fragmented and greatly vary across the EU. This study aims to develop a tool for assessing policy alternatives by reviewing existing national rare cancer policies, conducting interviews with experts, and analysing core stakeholders at the EU level. Results The main policy alternatives covered five domains: definition, registration, organisation of care, access to innovative therapies, and funding. Interviews revealed four policy options for each domain. Six core stakeholders were determined: patient organisations, healthcare professionals, researchers, industry, health legislators, and health authorities. A pilot policy assessment tool was developed on this basis. Lessons The pilot study coherently explored policy alternatives for rare cancers in the EU. Using these findings, policymakers and researchers can assess the impact of different policy options at a national level and contribute to the development of a unified EU policy framework for rare cancers. The pilot survey was also useful to collect input from the core stakeholders. Key messages • This study identifies key policy domains and feasible alternatives. A pilot preference assessment study based on these options can aid in EU policy development. • Navigating rare cancer policy complexities demands collaboration and innovation. Engaging stakeholders and exploring alternatives can forge a more effective EU framework for addressing rare cancers.