Gerbillon was born in Verdun, France, and entered the Society of Jesus in 1670. During his fourth year of theological studies in Paris, he volunteered to join five confreres designated to go to China as mathematicians of King Louis XIV. Arriving in Peking (Beijing) in 1688, Gerbillon and Joachim Bouvet were chosen to work at court. After teaching geometry to the emperor for a number of months, Gerbillon accompanied another Jesuit, Tomas Pereira, to Nerchinsk, Russia. As interpreters and negotiators, they were instrumental in concluding the 1689 Sino-Russian treaty, the first agreement in Asia based on the law of nations.
Gerbillon's eight trips to Mongolia and Manchuria are recorded in his travel accounts published in Europe. He completed Manchu and Chinese translations of French works on philosophy and geometry. As superior of the French Jesuits in China, he discussed the Chinese Rites issue with Charles Thomas Maillard de Tournon, the first papal legate sent to Peking. A rupture of relations between legate and the emperor ensued. Apparently, because Gerbillon, in the eyes of the emperor, had taken the side of Tournon, no imperial funds were allocated to defray Gerbillon's funeral expenses when he died.