The choice to include a train as the primary mode of transportation was inspired by a book Eiji Aonuma read to his son, "The Tracks Go On" by Fumiko Takeshita and Mamoru Suzuki. In this book, children lay down tracks for a train as it progresses across the countryside. A year of the game's two-year development time was spent working on the ability to lay down tracks before the feature was ultimately cut.

Upon exiting a dungeon with the Skull Engine, it will play one of 3 random short tunes with it's whistle:
• The Overworld Theme from The Legend of Zelda.
• The Overworld Theme from The Legend of Zelda: Spirit Tracks.
• The sound of a Phantom appearing.

Found within the game's data are 2 unused tracks from Phantom Hourglass, The Great Sea and Boss Battle themes. Both tracks use different instruments to the originals, along with added echo effects.

In the Japanese version of the game, several direct quotes refer to Tetra being Princess Zelda's grandmother.

There is a full 3D model of the entrance to the Temple of the Ocean King in Spirit Tracks' code. This model, of course, goes entirely unused although you do get to eventually visit the temple via a warp instead of the main entrance.