Yoshi's Story was the first Mario series game to be rated E for Everyone instead of K-A for Kids to Adults due to the changeover by the ESRB from the previously used K-A rating in 1998.

It is possible to collect 30 of one kind of fruit that isn't Melons in each level of the game, although collecting 30 of any fruit that isn't a Melon is much more challenging. At the start of the game, you spin a roulette to determine the "Lucky Fruit" for that playthrough, ranging from Apples, Bananas, Watermelons, or Grapes. Whichever fruit is picked as the Lucky Fruit will double the amount of that fruit featured in every level; normally there are 6 of each fruit in every level, meaning there are 12 of the Lucky Fruit in every level. If you want to gain 30 of one kind of fruit, it is best to do this with the Lucky Fruit you are assigned, and find ways to strategically use Heart Fruit to turn 18 enemies into the desired fruit whenever possible.

For doing this, there are different drawings in the level ending animation for every other fruit that changes to it accordingly if you got 30 of a certain fruit.

The Japanese version didn't have a Story Mode save feature. For this reason, the option to erase Story Mode's save data is absent in Japanese version.

The game was originally called Yoshi's Island 64, and featured a logo strongly resembling that of Super Mario World 2: Yoshi's Island for the SNES, suggesting that Yoshi's Story was originally going to be a sequel.

Hitting the Spiders with an egg in the uppermost hut of the Jungle Hut level affects the instruments used in the music that plays during the level.

The newspapers in the background of the Jelly Pipe level say a variety of things, such as Luigi, Mario, Zelda, N64, Pikachu, Nintendo, Yoshi, and Nintendo 64.

There's an unused piece of music that sounds similar to the tracks for when a page opens in story mode.

In prerelease footage of the game, a purple and brown Yoshi can be seen. They even appear in the intro. But for some reason, they were taken out of the game.