The European Union (EU) has an active role in the global and European multilevel human rights protection regime that comes from its primary law, such as the Charter of Fundamental Rights of the European Union. Children's rights protection in the multilevel setting of governance of the EU has a particular place and faces various challenges. In particular, the protection of children's rights in social, health and education legislation of the EU on the basis of the principles of conferral, subsidiarity and proportionality requires special attention. In our contribution, we aim to understand how the EU manages to ensure the protection of children's rights in these three policy fields and identify the main characteristics and challenges of its legal actions. The analysis is theoretical, combining the legal method of document analysis and qualitative data analysis of conducted interviews with a critical view on intersectoral policy coordination and a mainstreaming mechanism for children's rights. Our findings suggest that the EU's legislation in the social, health and education sectors, together with available specific policy tools and funding opportunities, ensures all necessary conditions to guarantee the mainstreaming and implementation of children's rights at the national level of governance. In addition, the growing awareness of the comprehensive nature of the protection of children's rights and concrete actions reflect a strong EU commitment to ensure the intersectoral policy coordination in the protection of children's rights in the EU.