Clock Tower is a point-and-click adventure game with 3D graphics. The player may use a PlayStation controller or mouse to move the cursor on the screen. The cursor changes shape when placed over certain objects, which the player can click to interact with. Clicking on any location guides the player character in that direction. Moving the cursor to the top of the screen reveals the player's inventory. Clicking on an item and then clicking on an object on the screen uses the item on that object or in that location. Some items such as keys are used automatically when clicked.
The player character has three levels of strength. The strength level is indicated by the cursor which will either be white, flashing yellow, or red. Strength will decrease after extreme actions or being attacked by the game's enemy, Scissorman, and recovers with time. When the character's life is being threatened, the cursor will blink red, indicating panic mode. If the character is being chased, click points are only effective on objects that will make Scissorman retreat. In escape mode, actions do not lower strength and recovery is suspended. This mode stays active until Scissorman is somehow forced to retreat. If the player's strength reaches zero, then it is game over and the player must continue from the last room they entered with one level of strength.
The game features four scenarios including the prologue. The actions during the prologue determine who will be the central character in the story, either Jennifer Simpson or Helen Maxwell. The scenarios and player characters that follow are determined by the player's actions. There are five different endings per heroine depending on how the scenarios progress. After each scenario is a save screen and an intermission mode that allows the player to explore without the threat of Scissorman. During the intermission, the player can have conversations with various characters. The next scenario begins after the required conditions of the intermission are met.