N64 vs. 3DS

Majora's Mask 3D (2015) follows the Nintendo 64 original closely but moves, swaps and adds a number of things. This list only contains differences confirmed by the game data behind this app. The map links below always point to the version you have selected in the app.

Rewards that changed

What	Nintendo 64	3DS
Great Fairy in Woodfall	Great Spin Attack	Extended Magic Power
Great Fairy in Mountain Village	Extended Magic Power	Great Spin Attack
Koume's boat archery	Piece of Heart	Empty Bottle
Dampé's chest under Ikana Graveyard	Empty Bottle	Piece of Heart
Oceanside Spider House	Giant Wallet only on day 1	Giant Wallet on any day
Bottles in total	6	7 (extra one from Gorman's Mystery Milk quest)

Things that moved

What	Nintendo 64	3DS
Bank teller	West Clock Town	South Clock Town
Bombers' Notebook	Jim, for winning the Bombers' hide-and-seek	The Happy Mask Salesman
Song of Soaring stone	End of the path to Woodfall, past the Deku Palace	Next to the Owl Statue at the swamp entrance
Goron Elder	Further from the Twin Islands	Closer to the Twin Islands
Shiro (Stone Mask)	Road to Ikana	Pirates' Fortress exterior
Giant's Mask	Chest in Twinmold's arena	Handed to you during the fight

Only on 3DS

Two fishing holes: Road to Southern Swamp and Zora Cape.
The Mystery Milk side quest with Gorman on day 2, which awards a seventh bottle.
Save statues in many areas and every temple (see the Owl Statues guide). They save but cannot be warped to.
Mikau can be healed for the Zora Mask on any day.
The Song of Double Time lets you pick the hour to skip to within the current day; on N64 it always jumps to the next 06:00 or 18:00.

Different item names

Nintendo 64	3DS
Land Title Deed	Town Title Deed
Circus Leader's Mask	Troupe Leader's Mask
Express Mail to Mama	Special Delivery to Mama

Schedules

Most people keep the same routine in both versions. Where the 3DS Bombers' Notebook shows a different window, it is noted in the relevant guide. Examples:

Madame Aroma waits in the Milk Bar from 18:00 on the final day on N64; on 3DS she is already there from 10:00.
The Anju & Kafei reunion starts at 04:30 on N64; the 3DS notebook lists it from 05:00.
Sakon's robbery happens 00:20–00:30 on night 1; the 3DS notebook lists 00:00–01:00.