This game is a throwback to 1980's arcade games, since the gameplay revolves around getting a high score, not finishing a story. Every play session takes place across two levels. In the first, Baby Mario is falling through the sky and the player must guide him down safely by drawing clouds on the touchscreen. After Baby Mario lands on Yoshi's back, the second level begins where the player must guide Yoshi through a side-scrolling level by drawing clouds until they meet up with Baby Luigi at the goal.
The game features four modes: Score Attack, Marathon, Time Attack, and Challenge.
This game features the following tropes:
- Arduous Descent to Terra Firma: During the start of a level, Baby Mario begins falling from the high skies (likely because the stork transporting him either accidentally released or got attacked like in the original game). At first, it seems to be a harmless descent (three ballons act as a collective parachute), but between the sky and the lush mainland of Yoshi's Island, there are Fly Guys, Briers, and Gusties aiming to burst the baby's balloons. The player has to draw Solid Clouds on the touch screen to guide Baby Mario and evade the enemies along the way until reaching the ground, where Yoshi awaits to grab the baby and escort him through the second half of the level. If all three balloons are burst, Kamek will appear to intercept Baby Mario and kidnap him, resulting in a Game Over.
- Auto-Scrolling Level: This is how Yoshi's levels in the game play. Yoshi continues to walk and that keeps the screen moving.
- Easter Egg: Totaka's Song can be heard during the windy stage if the player pauses the game and waits for three minutes and 45 seconds.
- Endless Game: Marathon and Score Attack modes only end if Baby Mario or Yoshi are defeated by enemies.
- In-Universe Game Clock: Yoshi's stages run through morning, day, evening, and night as the game continues.
- Minigame: If the player earns a high score in the Marathon and Score Attack modes, they unlock a minigame called Balloon Trip.
- No Plot? No Problem!: Even though the game is based on Yoshi's Island, there is no plot and the game has no tie-in to that game.
- Tech-Demo Game: Hiroyuki Kimura who directed the game, made it for the Nintendo DS because he wanted to create a simple game that made use of its gameplay interfaces.
