In Yu-Gi-Oh! R, Jonouchi, as usual, lends Yugi a hand when Anzu is kidnapped by Yako Tenma and KaibaCorp is taken over. Jonouchi provides his usual comic foil for the first few chapters, though he does get the key out of Tilla Mook. His first major role comes when he picks up a "Booby Trap" card that turns out to be a literal booby trap. Jonouchi (and Honda, who went in after him) is dumped down into KaibaCorp's basement where he has to face the third Card Professor, Klamath Osler, who he defeats by using "Roulette Spider" to make Klamath's own "Antlion" attack him.
Jonouchi later encounters a laboratory run by the fifth Professor, Pete Coppermine. Impressed that Jonouchi beat Osler, Coppermine bets Jonouchi 10,000 Yen that Jonouchi could not defeat him. Through clever use of Trap Cards, Jonouchi allows his "Divine Knight Ishzark" to attack twice, depleting Coppermine's Life Points with one move.
Jonouchi's next opponent before returning to the group is the seventh Professor, Mendo Cino. This duel is longer and more taxing to Jonouchi than the others, and even with the help of "Jinzo" he is not able to win easily. His victory comes when he uses "Stop Defense" to force Cino's "Guard Mantis" into Attack Position, and then striking it while it is weak. Cino, who had belittled Jonouchi throughout the duel over the fact that Jonouchi's tactics were inferior to his own, was impressed by his win and gracious in defeat.
Jonouchi's next Duel is against Reiko Kitamori, the tenth Professor. He has to intimidate her into dueling, but once he gets her angry, she proves to be his strongest opponent yet. He finally defeats her by using "Relentless Attacks" to allow his "Gilti-Gearfried the Magical Steel Knight" to attack twice. After this Duel, he is picked up by Mokuba and taken to the place where Yakou is by him.
Later, he has a rematch with Bandit Keith who has The Wicked Eraser and is able to beat him by using Keith's Time Machine which Jonouchi stole after beating Keith the first time in Duelist Kingdom arc. This is Jonochi's final Duel in Yu-Gi-Oh! R.