Harry Potter and the Chamber of Secrets follows the exploits of Harry during his second year at the Hogwarts School of Witchcraft and Wizardry. During his time there, Harry's classmates are coming under a mysterious paralysis and Harry must get to the bottom of what is happening.

The game involves Harry being given objectives to complete along with him having to go to class to learn spells. The game also has some mini-game diversions such as playing Quidditch, dunking gnomes in water, and collecting wizard cards.

Occasionally Harry will find himself in a combat situation. Harry can be equipped with up to three different spells at a time. If the player can make Harry cast a spell with correct timing, the spell will be more powerful than normal.

The PlayStation 2 version was ported internally by Electronic Arts instead of by Eurocom who developed the other console versions, hence the PS2 version sporting some noticeable differences. but otherwise keeping the majority of the game the same. Some differences include the PS2 version of the game having an overall lower difficulty level plus when Harry is riding a broom he can land it anywhere instead of only in designated landing spots. Speaking of platform differences, the GameCube version has an exclusive feature that allows the player to connect to the GBA game and unlock a new Wizard Card.