A variety of rights are involved in the legal status of faith schools. Among them are freedom of religion, freedom of teaching, and the parents’ right to have their children educated in accordance with their religion or belief. The protection of those rights require the recognition of a high degree of autonomy to faith schools, which in turn poses some challenges when put in connection with the well-established competences that contemporary States —representing legitimate societal interests— have in organizing the educational system to guarantee an appropriate education of the youth (a notion that includes not only the academic quality of education but also the transmission of certain values that are often deemed essential for the preservation of democracy). Faith schools’ right to have their own ethos and functional autonomy may sometimes be in conflict with the State self-understanding of its role in education. To reach a balance is often not a simple task, and the emergence of faith schools with a non-Christian ethos adds further complexities. A European perspective based on the ECHR may prove useful at the national level. The Court of Strasbourg has rarely dealt with faith schools issues, but there is a certain case law on religious autonomy and its limitations. The purpose of this paper is to analyse this case law and to examine to what extent it is possible draw some conclusions that clarify the delicate balance between the autonomy of faith schools and the State’s competences on education.