In the Middle Ages, reason and faith competed for access to truth. Following Abélard and Albert the Great, Thomas Aquinas, in the 13th century, chose to defend the autonomy of reason in relation to faith.

He borrows from Aristotle's thought the idea of an autonomous natural order, independent of the celestial order. The supernatural order indeed transcends the natural order, but it exists separately and precedes it. Therefore, for him, there are two ways to access the truth about the world and particularly about God:

How then to reconcile the two? In the Middle Ages, two traditions emerged for articulating the relationship between reason and faith: mysticism and religious rationalism.

Mysticism consists of excluding reason from faith. Faith is absolute, beyond reasoning, and should never be subjected to reason. If it contradicts reason, that's normal, and trying to fit revealed truths into the framework of reason is heresy. God is well beyond reason; in other words, there is no point in trying to explain Him. Therefore, philosophy is very poorly regarded. God would even be beyond human language: He would be the unnameable, the wholly Other. His will is absolute and arbitrary. Therefore, one should not seek to understand why God did this or that; obedience is the only appropriate attitude. In Islam, it is also said that one should not represent God or give Him an image. In the Christian world, a mystic like Meister Eckhart notably wrote in a Sermon: "All things have a why, but God has no why." For mystics, the only valid philosophy is that which comes directly from Revelation. Anything that does not come from it is neither true nor false but devoid of any truth value. The direct opposite of this thought is the one that states that only reason is right, and that all faith is nonsensical. This is absolute rationalism, which leads to atheism. However, such a current did not yet emerge in the Middle Ages.

For proponents of religious rationalism, there is a complementarity between reason and faith, representing the middle position. The truth can be known both by faith and by reason. And so, what is true in faith must also be true in reason, and vice versa. The truth is one, but it is accessible in two ways. Therefore, two sciences cannot contradict each other but complement one another: natural science or philosophy and sacred science or theology. If this is not the case, if a contradiction appears between reason and faith, it is either that one reasons poorly or that one misinterprets the Scriptures.

Thus, for Thomas Aquinas, "Faith is the assent of reason moved by the will in the absence of evidence." In other words, reason is capable of apprehending the world and God, rationally, up to a certain point. At this point, it encounters no more evidence. The will can then choose to believe, and thus go further towards the truth by faith, or not to believe. But faith is not a leap into the absurd. It is not a humiliation of reason.

This is the middle position, which seeks to reconcile faith and reason. True rationalism is not to reject everything that reason does not understand, but to think about the limits of reason. What goes beyond reason is not necessarily against reason. A quote from Pascal in the Pensées illustrates this mindset very well: "Two extremes: to exclude reason, to admit only reason."

The Christian Middle Ages were marked, at the beginning of the 13th century, by the birth and multiplicity of universities in the West. A university is a community of students and masters from the same city under the control of the Church and comprising in principle four faculties: arts, theology, law, and medicine. Theology is conceived as a science, modelled after Greek science.

In 1200, Philippe-Auguste established the University of Paris, which quickly became the most renowned university in Europe. In 1257, Robert de Sorbon founded a college of theology at the University of Paris, which would later be called the Sorbonne. A new method of teaching and research, known as scholasticism (from the Latin schola, meaning "school"), emerged within these universities. It involved the "disputatio," a type of debate in which participants presented opposing views to an audience. A thesis was proposed, followed by objections that required a response. Once all arguments were exhausted, the master would resolve the debate with a reasoned solution.

Among the great Aristotelian masters who marked this era, we can mention Albert the Great (1200-1280) and Thomas Aquinas (1224-1274). The latter, by establishing reason in its rights, highlighted the specificity and autonomy of philosophical wisdom in relation to theology. Just as grace presupposes nature and fulfills it, faith presupposes and perfects reason.

From then on, religious rationalism would definitively prevail over mysticism.