Jean Louis Bonaparte, known as Napoleon in the original Japanese language version, is a recurring character. His character is based on Napoleon I. In the English version, Bonaparte is voiced by Mike Pollock, while Naoki Tatsuta takes the role in the Japanese version.

Vice-Chancellor of Duel Academy beginning with the second season, Bonaparte is a stout man hailing from Paris, France who originally attempted to demolish the Slifer Red dormitory at every opportunity, but was repelled by Crowler. He later dueled alongside Crowler against Maximillion Pegasus for a job at Industrial Illusions, after they falsely believed themselves to be fired by Chancellor Sheppard. Following Duel Academy's arrival in an alternate dimension, he encourages the students to save his son Marcel from the Duel Spirit Yubel. Previously married, Bonaparte's son is in the custody of his ex-wife. After Marcel is rescued, Bonaparte apologizes for neglecting him and leaving his wife for his career, and the two return to France at the end of the season.

In both the English and Japanese versions, Bonaparte speaks French on occasion. In the latter, he also refers to himself with the archaic "wagahai," and ends the majority of his sentences with "de aru." In the English anime, he frequently uses the French terms "feux pas" and "au revoir."

Bonaparte plays a Toy Army deck, which includes cards that detail Napoleon I's conquests and coronation, such as the monsters Toy Soldier and Toy Emperor. His Toy Soldier cards are physically weak, but he supplements them through Forced March and Fife and Drum Corps, as well as a variety of Trap Cards.