Couperin was born in Paris. He was taught by his father, Charles Couperin who died when François was 10, and by Jacques Thomelin. In 1685 he became the organist at the church of Saint-Gervais, Paris, a post he inherited from his father and that he would pass on to his cousin, Nicolas Couperin. Other members of the family would hold the same position in later years. In 1693 Couperin succeeded his teacher Thomelin as organist at the Chapelle Royale (Royal Chapel) with the title organiste du Roi, organist by appointment to the King Louis XIV.

In 1717 Couperin became court organist and composer, with the title ordinaire de la musique de la chambre du Roi. With his colleagues, Couperin gave a weekly concert, typically on Sunday. Many of these concerts were in the form of suites for different instruments andharpsichord, on which he was a virtuoso player.

His two Masses for organ (and) are his unique works for organ and were published as his .

Couperin died in Paris in 1733.