The entire Forbidden Memories soundtrack is the one nigh-unanimously praised aspect of the game, and a big motivation for players to play through the Campaign mode to hear all the game's tracks (Free Duel uses a single music track across all opponents instead of the game's various tracks heard in Campaign).
- Seto Kaiba's battle theme, a techno song reminiscent of the Digimon World or Donkey Kong Country series.snakeisninja: Kaiba that son of a bitch gets the best cards AND the best music in the damn game! He gets a theme song, his own duel music, and variations of the first two for his future self! AND THEY ALL KICK ASS!
- Priest Seto's battle theme, a variation of Kaiba's battle theme that has a more orchestral quality to it.
- Seto's Betrayal and Seto Kaiba Face-Off, two awesome remixes of the same sinister tune.
- The duels against the High Mages, Sebek, and Neku. Tampini drums, trumpets, and an all-around frantic beat makes for a very intimidating boss fight.
- The battle against DarkNite/Nitemare is very shocking. As the theme of the Final Boss and True Final Boss, it has to be; you're fighting for the fate of the world to this theme.
- Egypt in Ruins, played when you return to the past and find everything you knew of your life is gone.
- Tournament Announcement music in the modern world setting. The drum beats and the sinister tune emphasize how the Kaiba Corporation Duel Monster Tournament is definitely not about children's card games.
- The Preliminaries Theme is quite catchy, serving to help get the player in the mood.