Spirit Tracks continues its style of gameplay from Phantom Hourglass, in which players use the stylus to control Link and use weapons and items. The game is divided into an overworld, which Link traverses using the Spirit Tracks, and towns and dungeons which he travels by foot. The player alternates between exploring the overworld and exploring towns and dungeons in order to complete the game's main story, but may opt to complete sidequests for further rewards. In the overworld and dungeons, the player is able to make notes on their current map as an aid in puzzle solving and continuing the story.
In the overworld, Link is able to direct his train across land, with the ability to control speed and forward or reverse direction, to turn at track intersections, and to blow the train's whistle to scare animals off the tracks.[2]: 30  The player is able to automatically set a route for the train by drawing on the map, though not all locations are immediately available. Later, Link is given a cannon that he can use to defend the train from attacks. Link also eventually gains a cargo car, which he can use to move goods between towns. Some missions require Link to transport a passenger along the rails and require the player to keep the passenger happy.
As the game progresses, the player opens more of the map. In towns and dungeons, the player controls Link using the stylus, directing the character where to go. The stylus is also used to perform attacks and dodges and to select items such as bombs and a boomerang, used for combat and puzzle solving. Certain items, in particular Zelda's pan flute, require the player to blow into the DS's microphone. In the case of the pan flute, completing songs can unlock new magical songs, reveal hidden secrets, heal Link, or restore more of the Spirit Tracks. In certain dungeons, the ethereal Zelda can inhabit Phantom Guardians. The player can direct the possessed Phantom along a stylus-drawn path to attack enemies or simply follow Link. Several puzzles of the game require the player to manipulate Link and the Zelda-possessed Phantom to complete a goal. In towns, the player can have Link speak to its residents, buy goods at local stores, and learn helpful tips.
Unlike The Legend of Zelda: Phantom Hourglass, Spirit Tracks does not feature Nintendo Wi-Fi Connection multiplayer. However, up to four players can also play via DS Download Play, using only one game card, and only one game system per player. This multiplayer mode is non-canonical, as all four players play as different Links, each with different-colored tunics (a style that was used in The Legend of Zelda: Four Swords Adventures). Each player attempts to collect as many Force Gems (of varying sizes, value and number) as possible within a set time limit. Opposition includes the other players, a varying number of non-partisan Phantoms, who will attack any player on sight; and the play stages themselves, with environmental hazards. Results of the most recent game played will show up on a bulletin in most in-game towns and cities. "Tag Mode", an item trading system, is also available between local players.[2]: 37