In Fruit Ninja, the player slices fruit with a blade controlled via a touch pad. As the fruit is thrown onto the screen, the player swipes their finger across the screen to create a slicing motion, attempting to slice the fruit in half. Extra points are awarded for slicing multiple fruits with one swipe, and players can use additional fingers to make multiple slices simultaneously. Players must slice all fruit; if three fruits are missed, the game ends, but upon reaching scores that are multiples of one hundred (i.e. 100, 200, 300, etc.), the player will gain an extra life (unless they have not missed a piece of fruit already). Bombs are occasionally thrown onto the screen, and will also end the game should the player slice them.
A mode known as Zen mode allows players to seek high scores without the hindrance of bombs appearing on the screen. Also available is an Arcade mode in which players have only sixty seconds to achieve a high score. Special bananas are added to the standard fruit which have unique bonuses such as doubling points scored for a limited time, increasing the amount of fruit on the screen, or slowing down the movement of all fruit for a short period of time. In Classic and Arcade mode, special pomegranates are occasionally thrown on screen. In Arcade Mode, it is guaranteed that at the end of each game that a pomegranate will appear. Players can slice these multiple times to get extra points. Similarly, an ultra rare pritayasometimes appears in Classic mode which, if sliced, awards players fifty points.
When Fruit Ninja celebrated its second anniversary, Halfbrick released an update with a new feature called Gutsu's Cart, which comprises two characters, a pig named Truffles and a human named Gutsu. In the various modes of the game, you can earn starfruit to purchase items in Gutsu's Cart. There are three purchasable items at the cart which are used in the game; Berry Blast causes sliced strawberries to explode and gives the player five extra points. Another item is Peachy Time: slicing a peach in Zen or Arcade mode gives the player two extra seconds. The third item is Bomb Deflect which enables the player to deflect Bombs upon accidentally slicing them. Starfruit can be obtained after each game, proportional to the score, or by slicing the semi-rare starfruit.