- The Recruit's Sword is the first of two swords acquired by Link in Spirit Tracks. Found in the training room of Hyrule Castle.
- The Lokomo Sword is the second and only other sword that Link wields on his journey. It is given to him by Anjean.
- The Shield is a standard shield that Link can purchase from numerous shops around New Hyrule for prices between 80 and 200 Rupees.
- The Shield of Antiquity is the only other shield usable by Link, and is obtained when he gets 10 Stamps in his Stamp Book and shows them to Niko.
- The Spirit Flute is Spirit Tracks's main instrument, and is used by Link to play magical songs. It is given to him by Princess Zelda in Hyrule Castle.
- The Whirlwind, found in the Forest Temple, is used to blow items and Phantoms possessed by Princess Zelda across chasms. It is also used to defeat the Forest Temple's boss, Stagnox.
- The Boomerang reappears in Spirit Tracks and is found in the Snow Temple. It is controlled similarly to its counterpart in The Legend of Zelda: Phantom Hourglass. It can be set ablaze by either blue or normal fire and can subsequently be used to freeze water or melt snow. Additionally, it is used to defeat Fraaz.
- Bombs can be purchased from Beedle's Air Shop for 100 or 500 rupees. They can also be found stray in areas on Link's journey, or within Item Bulbs.
- The Whip, a new addition in Spirit Tracks, is found in the Ocean Temple . It can be used in a similar way to the Grappling Hook, and can also be used to snatch objects from enemies. It is used to defeat the Temple's boss, Phytops.
- The Bow is obtained in the Fire Temple. Like the Boomerang, it is used in identical fashion to its Phantom Hourglass counterpart. It is used to defeat the Fire Temple's boss, Cragma.
- The Sand Wand is acquired in the Sand Temple, and can be used to temporarily raise blocks of sand in large pits. It can be used to make paths for Phantoms possessed by Princess Zelda as well as to defeat the Sand Temple's boss, Skeldritch.
- The Bow of Light is an upgrade to the standard bow and is acquired in the Tower of Spirits. It is with the Bow of Light's charged Light Arrows that Link can defeat Malladus, as well as activate Golden Eye Switches.
|Anjean · Byrne · Chancellor Cole · Link · Malladus · Princess Zelda|
—Full list of characters
|Stagnox · Fraaz · Phytops · Cragma · Byrne · Skeldritch · Demon Train · Chancellor Cole · Malladus|
| Fire Realm · Forest Realm · Ocean Realm · Sand Realm · Snow Realm|
—Full list of locations
|Forest Temple · Snow Temple · Ocean Temple · Fire Temple · Sand Temple · Tower of Spirits|
|Lokomo Sword · Rail Map · Recruit's Sword · Recruit Uniform · Spirit Flute · Spirit Tracks · Spirit Train · Stamp Book · Tears of Light|
|Boomerang · Whip · Whirlwind · Bow · Sand Wand · Bow of Light|
|Anouki · Demon · Goron · Hylian · Lokomo|