| # | Title | Artist | Length |
|---|
| 1 | The Slitherers | Shota Kageyama | 0:45 |
| 2 | Hideout | Minako Adachi | 1:36 |
| 3 | Five Furious Strikes! | Shota Kageyama | 0:56 |
| 4 | Countdown to Destruction | Shota Kageyama | 1:21 |
| 5 | Dive | Minako Adachi | 2:41 |
| 6 | Trainers' eyes Meet (Scuba Diver) | Shota Kageyama | 0:57 |
| 7 | Team Aqua Appears! | Minako Adachi | 1:04 |
| 8 | Battle! (Team Aqua / Team Magma Leaders) | Minako Adachi, Hideaki Kuroda | 2:26 |
| 9 | The Super-Ancient Pokémon Awaken! | Hideaki Kuroda | 1:05 |
| 10 | Drought | Minako Adachi | 0:58 |
| 11 | Heavy Rain | Minako Adachi | 1:10 |
| 12 | Sootopolis City | Shota Kageyama | 2:00 |
| 13 | Cave of Origin | Minako Adachi | 1:37 |
| 14 | Battle! (Primal Reversion) | Minako Adachi, Hideaki Kuroda | 1:39 |
| 15 | Coexistence | Shota Kageyama | 3:51 |
| 16 | The Eon Flute | Hideaki Kuroda | 0:05 |
| 17 | Soaring Dreams | Shota Kageyama | 2:37 |
| 18 | Soaring Illusions | Shota Kageyama | 3:09 |
| 19 | Trainers' eyes Meet (Swimmer♀) | Minako Adachi | 0:29 |
| 20 | Ever Grande City | Minako Adachi | 2:18 |
| 21 | Victory Road | Shota Kageyama | 1:48 |
| 22 | Trainers' eyes Meet (Ace Trainer) | Minako Adachi | 1:05 |
| 23 | Rival's Theme | Minako Adachi | 1:25 |
| 24 | The Elite Four Appear! | Minako Adachi, Hideaki Kuroda | 0:53 |
| 25 | Battle! (Elite Four) | Shota Kageyama | 2:02 |
| 26 | Champion Steven | Shota Kageyama | 1:07 |
| 27 | Battle! (Steven) | Minako Adachi, Hideaki Kuroda | 2:13 |
| 28 | Victory! (Steven) | Minako Adachi | 1:09 |
| 29 | Room of Glory | Minako Adachi | 1:15 |
| 30 | The Hall of Fame | Shota Kageyama | 1:21 |
| 31 | Let's Go Home | Shota Kageyama | 1:47 |
| 32 | Ending Theme | Shota Kageyama | 7:00 |
| 33 | The End | Shota Kageyama | 3:31 |
