The article discusses the problem of prevention of radicalisation in religious schools in Europe. In this publication the authors of the publication aim to present a systematic analysis of the legal framework of religious education and its relationship and limitations in the aim to prevent radicalization. In order to achieve the aim of the research the following tasks will be carried out: revealing of the essence of the freedom of right of thought, religion and conscience and their relation to religious education; analysing documents, strategies and policies addressing the prevention of radicalization in Europe; evaluating the intersection of right to religious education and the need to prevent radicalisation. The question is relevant due to the ever-increasing number of terrorist acts performed by persons who have been born in European states (so called home-grown terrorists). The publication discusses the right to religion and the right to religious education and its limitations. The development of EU policy in the field of counter-terrorism and counter-radicalisation is extensively discussed. Finally, the guidelines are drawn for the conciliation of the freedom to religion and beliefs and the pressing need to prevent persons from radicalisation.