Jaden Yuki, known as Judai Yuki (遊城十代, Yūki Jūdai) in the Japanese version, is a student at Duel Academy and the protagonist of Yu-Gi-Oh! GX. He is a headstrong Duelist who aspires to be a Duelist as great as his mentor, Koyo Hibiki.
Jaden heard that the trainee teacher, Mr. Ryuga, had been taking cards from students he defeated, including Syrus Truesdale. Enraged by this, Jaden challenged Ryuga to a Duel, which Crowler sanctioned as the last necessary Duel Ryuga needed to win before becoming a teacher. Unbeknownst to Jaden, Ryuga cheated by using a ring that disabled the Duel Disks ability to read Spell Cards. However Jaden won by combining his Monster and Trap Cards and damaged Ryuga's ring with his final attack.
Jaden tried borrowing the Battle City DVD from Alexis Rhodes, only to find she had lent it to somebody else. Bastion Misawa, who had grown jealous of Jaden's card drawing ability and friendship with Alexis, had both the Duelist Kingdom and Battle City DVDs. Bastion challenged Jaden to a Duel, waging a loan of the Duelist Kingdom DVD for Alexis' contact details. Alexis arrived to give Jaden the Battle City DVD shortly before Jaden won. When she heard that Bastion had the Duelist Kingdom DVD, Jaden suggested that she and Bastion share contact details. Despite winning the Duel, Jaden had to allow Alexis to watch the Duelist Kingdom DVD, before he could borrow it.
Being the only student who hadn't voted in the 2004 Miss Duel Academy pageant, Jaden was urged to make to the tiebreaking vote between Seika Kohinata and Alexis. Seika challenged Jaden to a Duel for his vote, but Alexis refused to have someone else make her decisions. Instead Jaden and Alexis dueled under the condition that Alexis could withdraw from the competition if she won and Seika would get Jaden's vote if Jaden won. Although Jaden won, Seika said it wouldn't be right for her to accept Jaden's vote after the fight Alexis put up.
Crowler misinterpreted an exam score sheet and thought Syrus had scored a 0. He also took note of how Jaden hadn't passed a single written exam. As punishment, he arranged a Duel between Jaden and Syrus, where Syrus would be expelled if he lost and Jaden would have his Deck confiscated if he lost. Jaden initially tried to somehow avoid the Duel, but Syrus insisted that he wanted to proudly Duel someone he respected and become stronger. Although Syrus put up a strong fight, Jaden painfully pushed himself to win. Before Crowler could expel Syrus, Midori Hibiki arrived and explained the misunderstanding. She also asked to see Jaden, who really failed the test, to arrange a resit.
Jaden took part in the main tournament of the series, where he loses to Chazz in the finals. Although he defeated Chazz earlier, Chazz was able to overcome him in the rematch.
Following his defeat to Chazz, Winged Kuriboh led Jaden to the Abandoned Dorm, where he found Midori Dueling Mackenzie. Seeing Jaden, Midori attempts to comeback from a duel she was going to deliberately lose but is unable to win by that point. After the Duel, Jaden is powerless to save her from succumbing to the shadows. However, Jaden is able to defeat Reggie in a Duel, freeing her from the influence of Tragoedia and reviving Midori. Jaden seemingly ceases to use Koyo's Heroes after this Duel, and instead uses a Deck of his own design containing the "Masked HERO" series, though he does retain "Winged Kuriboh".
Jaden and Chazz confront Tragoedia at the warehouse by the docks, and they Duel as a team against him. Though they gain an early advantage, Tragoedia comes back with a wide array of cards that he designed himself. Pushed into a corner, Chazz leaves Jaden his face-down "Hopeful Future", knowing the outcome of the Duel will be determined on the next turn. Jaden combines "Winged Kuriboh" with "Light and Darkness Dragon" to create "Ma'at", which lends its power to defeat Tragoedia. The spirits of "Winged Kuriboh" and "Light and Darkness Dragon" sacrifice themselves to seal Tragoedia permanently. Years later, after graduation, Jaden faces a revived Koyo for the world title.
Jaden uses an "Elemental Hero" Deck, different from that of his anime counterpart. The Deck once belonged to Koyo Hibiki, but Jaden had modified it throughout the years. Though he later switches to "Masked Heroes" as he felt that he dishonored Koyo while Dueling Reggie MacKenzie, Jaden uses this Deck once more against Tragoedia, wanting to symbolically stand with Koyo to defeat the monster that put him into a coma.