Born in Rouen and educated in the Jesuit college of Caen, Huet was a noted literary scholar and linguist. He alternated between Paris and Caen for most of his life, but spent a year in the court of Queen Christina of Sweden in 1652 (two years after Descartes’ death there). He returned to Caen to work on an edition of Origen's commentaries, having found some rare texts of his in Sweden. In 1662 he helped found an academy of science in Caen. Huet was appointed tutor (sous-précepteur) to the dauphin (under précepteur Jacques Bossuet) in 1670 and elected to the French Academy in 1674. He was named Abbé d'Aunay in 1680, shortly after his ordination, and then nominated bishop of Soissons in 1685. However, as a result of troubles between Paris and Rome, his consecration at Soissons never took place. Instead, he was named bishop of Avranches in 1689, a position he assumed in 1692. He resigned his bishopric and took on the title of Abbé de Fontenay in 1699, retiring soon thereafter to the Paris house of the Jesuits that held the huge personal library he had bequeathed to them (and which ultimately was incorporated into the collection of the Bibliothèque Nationale). Huet died there in 1721 after a remarkably long life.

Huet reported in his Mémoires (1718) that he was initially a supporter of Cartesian philosophy but that he turned against it once he realized that “it was a baseless structure that tottered from the very ground.” He became disenchanted with Descartes’ philosophy because of its disdain for humanist values, the study of history, geography, and dead languages. This change of opinion resulted in Huet's critique of Descartes, the Censura philosophiae cartesianae (1689), whose chapters discuss a wide range of Cartesian topics, including doubt, the cogito, the criterion of truth, the human mind, arguments for the existence of God, body and void, the origin of the world, and the cause of gravity.