Heavenly Guardian is a scrolling shooter similar to the Pocky and Rocky series. The game's story involves Sayuki, the game's protagonist, who must save her beloved from a curse by finding the correct ingredients for a cure. The game can be played either singleplayer or multiplayer with another person. Sayuki is also followed by Toto, her pet snow rabbit, which can shoot freezing shots at enemies.
The gameplay involves moving Sayuki (or Koyuki in multiplayer) in any direction using the Nunchuck on the Wii or the Analog Stick on the Playstation 2. In two player mode, it is a contest to see which of the sisters can destroy the most ghosts and collect the most snowballs in their path. The Playstation 2 version also features a unique feature that allows players to perform a special boss attack once they beat a boss.