Klonoa: Door to Phantomile is a side-scrolling platform game viewed from a 2.5D perspective. The player moves the protagonist, Klonoa, along a path in a two-dimensional fashion, but the game is rendered in three dimensions. This allows the path followed to curve and for the player to interact with objects outside of the path. The game is divided by levels called Visions, where the player progresses by following a path with defeatable computer-controlled enemies and puzzles that must be solved.

At the end of some levels, the player must defeat a boss - a powerful enemy. The player defeats enemies by utilizing Klonoas weapon, the Wind Bullet, a ring that fires a burst of wind. If the wind hits an enemy, Klonoa lifts the enemy above his head. From this position, he can throw the enemy into another enemy to defeat them, or use the enemy to perform a double-jump (a jump of increased height allowing for new locations to be reached). If the player holds the jump button, Klonoa floats in mid-air for a short duration, which increases the jump length. Environmental factors such as small, localized tornadoes and springboards launch Klonoa up or forward, allowing the player to overcome obstacles.