It was established in 1204, but became famous as an educational institution when its discipline was reformed in 1602 by its abbess Jacqueline Arnauld. The Arnauld family became its patrons and the convent's subsequent history was directed by a number of the holders of that name. In 1625 most of the nuns moved to a new Port-Royal in Paris, which subsequently became Port-Royal de Paris while the older one was known as Port-Royal des Champs.
At the original site, several schools were founded, which became known as the "Little Schools of Port-Royal." These schools became famous for the high quality of the education they gave. In 1634, Jean du Vergier de Hauranne became director of the convent; he was a follower of Jansenism and from that point forward the convents and schools of Port-Royal became intimately associated with that school of theology.
The atmosphere of serious study and Jansenist piety attracted a number of prominent cultural figures to the school. The playwright Jean Racine and the theologian and mathematician Blaise Pascal were products of Port-Royal educations, and Pascal defended the schools publicly against the Jesuits in the Jansenist controversies within the Roman Catholic Church.
However, as a result of the Jansenist purges in Catholicism, the schools of Port-Royal were regarded as tainted with heresy. In 1679, the convent was forbidden to accept novices, heralding its eventual dissolution. The convent itself was decreed abolished by a bull from Pope Clement XI in 1708, the remaining nuns were forcibly removed in 1709, and the buildings themselves razed in 1710. A celebrated history of Port-Royal and its influence was written by Charles Augustin Sainte-Beuve in 1859.