Prince Jean-Christophe was born in Saint-Raphaël, Var, France. He is the son of Prince Charles Napoléon and his first wife Princess Béatrice of Bourbon-Two Sicilies, daughter of the late Prince Ferdinand of Bourbon, Duke of Castro, a claimant to headship of the former Royal House of the Two Sicilies. His parents divorced on 2 May 1989, two months before Jean-Christophe's 3rd birthday.
Jean-Christophe is the great-great-great-great-nephew of Emperor Napoleon I (who has no legitimate direct descendants) through the emperor's youngest brother, Jérôme, King of Westphalia. Through his mother, he is a descendant of King Louis XIV of France and through his great-grandmother, Princess Clémentine of Belgium, he descends from William IV, Prince of Orange, Charles III of Spain, Frederick William I of Prussia, George II of Great Britain and Louis Philippe I, King of the French, who was the last king to rule France, while his great-great-grandfather was Prince Napoléon Bonaparte, the heir of the Emperor Napoleon III, France's most recent monarch.