Baillet was born June 13, 1649, at La Neuville-en-Hez, a small town between Beauvais and Clermont (Oise), the eldest of seven children from a second marriage. His parents were of modest fortune. He was educated at the College and Grand Séminaire (1670) of Beauvais and ordained as a priest in 1676. After a few years as village priest he was offered a job as librarian of François-Chrétien de Lamoignon (1644–1709), a literary patron and collector of books. Baillet remained in Lamoignon's service until he died January 21, 1706. Although Baillet is now known mainly for his biography of Descartes (1691), he published not only learned compilations like Jugements des savants sur les principaux auteurs (1685) but also historical works such as Histoire de Hollande (1690) and books on piety and devotion, including Dévotion à la Vierge (Paris 1693) and Vies des saints (Paris 1701). These works came under criticism from the church, which placed them on the Index because it found Baillet's approach to hagiography too critical.

According to Baillet's biographer, it was his friend Abbé Jean Baptiste Le Grand who, “together with other interested parties” (possibly Lamoignon), asked Baillet's help in arranging the notes he had collected on Descartes. Baillet in turn introduced Le Grand to Abbé Claude Nicaise (1623–1701), an erudite with connections all over Europe (Baillet to Nicaise, April–May 1689, BNF fonds français 9361, 172–73). At that stage it was still Le Grand's project. Eventually they arrived at a division of labor: Le Grand would work on a new edition of the works and letters, the material for which had been given him by Clerselier, whereas Baillet would concentrate on a biography. It took one year to write the biography – the new edition never materialized. An abridged version of the biography, which on some points provides a different story, was published two years later (1693).