Ganondorf also appears in the 2001 Nintendo GameCube release Super Smash Bros. Melee as a hidden character in his Gerudo thief form, and not the giant pigman demon that he has traditionally been depicted as. He's Ganondorf from right out of The Legend of Zelda: Ocarina of Time. To unlock him one must either play 600 versus matches or defeat Event Mode Challenge #29, "Triforce Gathering", in which the player controls Link and faces off against Zelda and Ganondorf. After either of these conditions are met he will challenge you to a fight, and if you win you can choose Ganondorf as a playable character. In fact, to date this is Ganondorf's only playable appearance.

As a playable character Ganondorf is one of the largest and bulkiest fighters and shares an overall fighting style with the F-Zero champion Captain Falcon. On the other hand, however, he does wield some devistating attacks, such as his explosive kick and power punch. Like the other characters in the game, Ganondorf has his own unique "Break the Targets" round. His target arena is lined with spikes and fast-moving platforms. He's also a power hitter in the "Home Run Contest" and can easily smash the target around before belting it nearly out of the park. He also has no stage of his own and shares the Hyrule Temple level with Zelda.