Charles Ancillon studied law at Marburg, Geneva, and Paris, where he was called to the bar. At the request of the Huguenots at Metz, he pleaded its cause at the court of Louis XIV, urging that it should be excepted in the revocation of the Edict of Nantes, but his efforts were unsuccessful, and he joined his father in Berlin. He was at once appointed by the elector Frederick "juge et directeur de colonie de Berlin." Before this, he had published several works on the revocation of the Edict of Nantes and its consequences, but his literary capacity was mediocre, his style stiff and cold, and it was his personal character rather than his reputation as a writer that earned him the confidence of the elector.
In 1687 he was appointed head of the so-called Academie des nobles, the principal educational establishment of the state; later on, as councillor of embassy, he took part in the negotiations which led to the assumption of the title of king by the elector. In 1699 he succeeded Pufendorf as historiographer to the elector, and the same year replaced his uncle Joseph Ancillon as judge of all the French refugees in Brandenburg.
Ancillon's is mainly remembered for what he did for education in Prussia, and the share he took, in co-operation with Leibniz, in founding the Academy of Berlin. Of his fairly numerous works the one of most value is the "Histoire de l'etablissement des Francais refugies dans les etats de Brandebourg" published in Berlin in 1690.