Clock Tower 3 is a survival horror game played from a fixed third-person camera perspective in which players control 14-year-old school girl Alyssa Hamilton. Clock Tower 3 is the first game in the series to incorporate direct control over the protagonist, as opposed to the point-and-click gameplay used in the previous games. To progress through the game, the player must find items to unlock new areas, solve puzzles, and flee and hide from enemies ("Subordinates"). Eventually, each Subordinate must be defeated in battle. Throughout each level, the player also encounters the spirits of innocent people slain by the Subordinates. These spirits will attack Alyssa if she approaches them. In order to pacify them, an item of sentimental value must be found and returned to the spirit's corpse.
Alyssa is given no weaponry during the majority of the game, other than a limited supply of holy water, which can be used to temporarily stun pursuing Subordinates. Within each level, the Subordinate can appear in any location after a set period of time, but also randomly or if Alyssa makes noise. They also appear in certain set locations. When one appears, it immediately begins to chase Alyssa, attempting to kill her. The player must either hide from or evade it. Evasion can only be accomplished in certain places, and each evasion point can only be used once. Using an evasion point does not kill the Subordinate, but instead renders them unconscious for a set amount of time. The primary means of eluding one, however, is by hiding. There are multiple hiding points throughout each level, and each one can be used multiple times. However, hiding places are ineffective if the Subordinate sees Alyssa enter them.