Sonic Advance 3 contains several hidden unlockables and fun easter eggs that add to the game's replay value and charm. Discovering these can be a rewarding experience for dedicated players.

- Sound Test: Complete the game with the true ending (defeat Ultimate Gizoid with all 7 Chaos Emeralds) to unlock the Sound Test option in the main menu. Here, you can listen to all the game's music and sound effects.
- Boss Rush Mode: Also unlocked after completing the game with the true ending. This mode allows you to challenge all the game's bosses consecutively, testing your combat skills and aiming for high scores.
- Character Unlocks: As detailed in the 'Unlocking Characters' section, Knuckles, Amy, and Cream are unlocked by progressing through the main story and defeating specific bosses. These are not strictly 'hidden' but are significant unlockables.
- Secret Messages: Occasionally, if you leave the game idle on the title screen or certain menu screens, you might see small, humorous messages or character animations.
- 'A' Rank Rewards: While not a direct unlockable, achieving 'A' ranks on all acts and bosses is a significant achievement that the game tracks, providing a sense of completion and mastery.
Exploring every nook and cranny of each zone, and replaying the game with different objectives, is the best way to uncover all these hidden gems. The true ending and Boss Rush Mode are particularly rewarding for dedicated players.