The sustainability transition of rural areas is a must due to rapid climate changes and biodiversity loss. Given the limited resources of rural communities, policy should facilitate a just sustainability transition of the EU rural areas. The analysis of EU development policies, past performance and the envisaged scope of reform, presented in this study point to a serious inconsistency between the declaration and implementation of relevant policies. Namely, the marginal role rural areas perform in common agricultural policy and cohesion policy; a result of the lack of a complex approach to rural development. The analysis was based on the concept of good governance and took a multi-level perspective. It advocates territorial justice as an approach that should be at the core of creating a comprehensive policy for rural areas in the EU, including their diversity and empowering local communities to choose the transition pathway that is most in line with their current situation and development capacity. This analysis fills a gap in research on the evolution of the rural development policy in the EU. This research can inform the reprioritization and intensification of efforts to create equitable policies for EU rural development.