The game combines exploration and combat. Both elements make use of the Prince's acrobatic capability and agility. Throughout much of the game, the player must attempt to traverse the palace by running across walls, ascending or descending chasms by jumping back and forth between walls, avoiding traps, climbing structures and jumping from platform to platform, making other types of well-timed leaps, solving puzzles and using discovered objects to progress. There are also a few on-rails sequences where the Prince must ride a chariot along a long stretch of road at a dangerous, fast speed, requiring the player to avoid obstacles and fend off enemies along the way.
During combat, many of the same moves vital to the player in other situations can be put to use to overpower enemies. An example is the ability of the Prince to jump off walls in order to strike enemies decisively. The player generally attacks enemies and blocks using a dagger, although other objects or factors, such as the Dagger of Time and its time-control abilities eventually prove to be critical to victory. The Dagger of Time can also be upgraded by disabling "sand gates" that enemies may use to summon reinforcements, which will increase the number of sand charges it can hold for its powers and eventually unlock two new abilities that consume multiple sand charges to damage or destroy multiple enemies at once. Continuing the freeform fighting style employed in Warrior Within, the Prince can also obtain secondary weapons from defeated enemies or weapon racks and use them in dual wield combat, with most weapons having limited durability and becoming unusable after a certain amount of hits, or after they are thrown as projectiles or dropped when the Prince turns into the Dark Prince. The Wii version of the 2007 port, Rival Swords, implements attacks with generic shakes of the Wii Remote and Nunchuk, with the former swinging the Dagger and the latter swinging the equipped secondary weapon.