This study investigated the tension that exists between promoting an educational agenda and practising an educational approach which emphasises autonomy within the framework of religious education. Our main thesis is that every educational deed contains a dialectical tension between endorsing an educational agenda and the promotion of autonomy. Moreover, this tension is not restricted to religious education. The intensity of such a conflict varies in accordance with the flexibility (or inflexibility) of the dogma, the conceptual cohesion of the educational agenda and the perceived importance of granting autonomy to students. The more cohesive and inflexible the educational agenda is, the greater the danger that autonomy will be discarded. The present research examined an educational reform implemented in the National-Religious School Network in Israel, which included the promotion of autonomy among principals, teachers and students. Conducted over a six-year period (2006-2012), the research employed both qualitative and quantitative methodologies and involved various stakeholders in the school network. The multifaceted picture that emerged of the relationship between educational autonomy and religious agenda is presented.