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What is freedom of conscience? This article addresses the meaning and uses of this principle born at the time of the Reformation and which resurfaced in the nineteenth century as the school system was being secularised. Studying secularism in the light of this Protestant principle enables us to consider secularism as a means to call into question the school institution as a whole. A secularism that frees conscience, or at least safeguards freedom, does not only refer to the institutional organisation of relations between the religions and the state. It also allows for reflections concerning the political, religious and pedagogic forms apt to fulfil the Republic’s self-imparted mission since 1789: the emancipation of the citizens within a republican common.