Yoshi is available as a character in Paper Mario: The Thousand-Year Door. He is acquired originally as an egg by using Mario's paper airplane ability to fly to the top of Mr. Hoggle's hot dog stand in Glitzville. Yoshi's egg only appears after Mario and co. reach Rank 11 in the Glitz Pit, and hatches after Mario and co. lose to the Armored Harriers. Yoshi's color will change depending on how long after he hangs out with Mario. His first is the traditional green with red hair and an orange diaper with white polka dots. The user has the ability to name him, the first occurrence in the Paper Mario games. If the user decides not to give him a specific name, he will just be called "Yoshi".

In battle, Yoshi can Ground Pound a specific enemy a certain number of times. It stars out four times, but goes up to five, then finally six after he is upgraded. He can also Gulp enemies and spit them out, which is necessary to defeat the Armored Harriers. Yoshi can also throw eggs to make the enemies tiny. This ability is only available as an upgrade via Shine Sprites. Another upgrade is "stampede", where Yoshi summons many other Yoshis to run over the enemies, also only possible with Shine Sprites, and only after bringing the upgrade wizard the up arrow so he can get his red crystal ball out of his attic.

Outside battle, Mario can ride on Yoshi, which is traditional. Yoshi moves faster than Mario, despite Mario's weight. Yoshi can also use his hover ability to cross large gaps, making him the successor to Parakarry. His successor in Super Paper Mario is Peach.

Yoshi can also speak in this game, a rare occurrence. His only other speaking part was in Super Mario World, giving the message "Thank you for rescuing me. Bowser trapped me in that egg." He almost always says his name otherwise. He has a spunky personality, and refers to Mario by his nickname at Glitzville, Gonzales, having never originally heard Mario's name before then. As the game progress, though, he slowly realizes Gonzales is not his actual name.