Le Clerk was born in Geneva, where his father, Stephen Le Clerc, was professor of Greek. The family originally belonged to the neighborhood of Beauvais in France, and several of its members acquired some name in literature. Jean Le Clerc applied himself to the study of philosophy under Jean-Robert Chouet (1642-1731) the Cartesian, and attended the theological lectures of Philippe Mestrezat, François Turrettini and Louis Tronchin (de) (1629-1705). In 1678-1679 he spent some time in Grenoble as tutor in a private family; on his return to Geneva he passed his examinations and received ordination. Soon afterwards he went to Saumur.