While the storyline is virtually the same as the original, it does have its own differences, including voice acting, and some visual graphics. The game now has the same name in all territories as opposed to the original release in Europe and Australia, as Nintendo now have secured the rights to the Star Fox title.
- It is now possible to save between missions, instead of having to complete all seven in one try.
- The sound quality has been greatly improved over the original; in addition, the soundtrack has been modified.
- While the N64 version only had English and Japanese dubbing (plus the Lylat language only available in Star Fox 64's PAL version : LylatWars), the remake has been dubbed into many languages, mostly European (like Spanish, Italian, or French). The Lylat language voice option is now no longer present.
- The introductory text now says, "STAR FOX ON NINTENDO 3DS" instead of "STARFOX IN NINTENDO 64"
- Training Mode is now required to be completed at least once before the story can be attempted.
- The Training Mode instructor now has spoken dialouge, as opposed to speaking just the Lylat language in the original.
- The 3DS gyroscope can be used to control the Arwing/Landmaster/Blue Marine in place of the Circle Pad
- Upon playing the main mode once, a new Score Attack mode is unlocked, allowing the player to replay levels and attempt to beat their best score, instead of having to beat the whole game in one go.
- In addition to the original script, there are also slight alterations; eg, in the Sector Y level in the original version, Slippy mentions "Something's wrong. I don't see anything." In the remake, it is changed to "Something's wrong. I don't see the enemy fleet." Falco, when being hit by Fox, says "Hey genius, I'm on YOUR side!" instead of "Hey Einstein, I'm on YOUR side!" Various lines were added in to the remake that were not in the original version; eg, after managing to pull off a second sommersault against Wolf, Wolf will now say "Seriously?" in addition to saying "What the heck?!" and after a third, he will say "Oh, dang it!" Peppy, when hit by Fox a second time after a few seconds, will now say "Fox, it's me! Peppy!" in addition to saying "Knock it off, Fox!" and after a third, he will say "You're making me nervous, Fox!" and after a fourth, he will say "Agh! Fox!". Another example is when the boss of Corneria (alternate mission) says 'Charge!' instead of 'Deploy all units! Charge!'
- In the opening cinema, James McCloud is not holding a blaster.
- The Arwing's status can be seen on the touch screen; eg, laser type, and if wings are broken.
- In the ending, General Pepper offers Star fox to join the Cornerian Army but Fox interruped the offer and turned him down. But in the 3D version, Fox lets General Pepper finish his sentence before declining the offer.
- In Area 6, Gorgon's hyper beam is now red instead of rainbow colored.
- The Cornerian Army logo from Star Fox: Assault is present in the audience chamber where team Star Fox meet General Pepper after the end of the war.
- The graphics have received a major improvement over the original, in addition to being displayed in stereoscopic 3D (when it is toggled on).
- All major bosses now have their name and a brief description displayed at the start of each fight
- The physical design of Bolse has changed, making it look more like a traditional satellite
- Corneria now has viewable landmasses and oceans
- There is no green haze surrounding Venom.
- Zoness now possesses rain. Similarly, in Fichina, it is now snowing.
- Sector Y is changed from green/yellow to purple/orange in the actual level and bluish yellow in the mission select screen. Similarly, Sector Z has a more dark purple shade compared to the original game's orange.
- The Training mode now resembles a VR simulation instead of a realistic space city.
- The destruction of various bosses are significantly more fast-paced.
- The planet Fichina has its correct name displayed, as opposed to being named Fortuna in the western territories.
- The color of the background when fighting Andross is changed to red. In addition, Andross no longer appears in shadow when first seeing him.
- The Great Fox's tail fin looks like that from Star Fox: Assault.
- The wings on Bill's Cornerian Fighter are tilted upward like in Star Fox Command.
- If the Great Fox gets hit by a missile in Sector Z, the wing will be broken instead of completely being blown off like in Star Fox 64.
- Each of the two warp stages, one in Meteo and the other in Sector X, have different background colors, instead of both of them having the same color, green and yellow. In Meteo, the warp background color is orange; for Sector X, magenta or pink.
- The Landmaster resembles its Super Smash Bros Brawl apperance.
Battle Mode serves as Star Fox 64 3D's multiplayer component and has been completely reworked for the Nintendo 3DS. Battle Mode can either be entered in single player or a lobby can be hosted in which other local players can join via download play. Players are given the option to display live video of themselves in game using the 3DS's inner facing camera instead of the respective Star Fox pilot. Like the original game, up to four players can compete in a match, however, empty slots can now optionally be filled with AI controlled enemies.
Arwings are now distinguishable by different ship, laser, boost, and powerup coloration. Additionally, in contrast to story mode, barrel rolls now fill up the boost meter slightly. Any player or AI opponent with a score higher than the player will be marked with a crown. Three different gametypes are available: Survival, Points Battle, and Time Battle. In Survival, every player has only one life; if multiple players are left when the time runs out, the round will proceed to sudden death. In Points and Time Battle players battle to a set score and time limit, respectively. Each gametype can be customized to an extent.
- Time/Points Limit: Time can be set to 2, 3, or 5 minutes in Survival mode and 3, 5, or 7 minutes in Time Battle. In Points Battle no time limit is present and the match will instead end at 3, 5, or 7 points.
- Items: Can be set to either Classic or Power-Ups.
- COM: Enable AI controlled Arwings and select difficulty. Available options are Off (only when other players are present), Normal, Advanced, and Expert.
- Stage: Macbeth, Meteo, Corneria, Venom, or random selection.
- Player Icons: Choose whether enemy icons are displayed Always or only when enemies are Nearby.
- Shield Gauge: This option only affects the player and serves as a handicap function to new players, or provide a greater challenge for more experienced players. Can be set to Normal, Small, or Large.
When Items is set to classic, only items that were present in the original game will be at the players' disposal. These include the star, silver rings, wing repair, laser upgrade, and smart bomb. When toggled to Power-Ups, mystery boxes not unlike Mario Kart's items will be scattered throughout the map. In addition to smart bombs now being a possible outcome, there are several different unique weapons available from these boxes.
- Force Field: Protects the user from any incoming projectiles. The player can still take impact damage from colliding with other Arwings or buildings.
- Cloak: Renders the player completely invisible, including on radar.
- Smart Bomb
- Dead Weights: Releases multiple sandbur-like objects that latch onto enemy ships to slow and weigh them down. If you find yourself under the effect of Dead Weights, pressing L and R rapidly in succession detaches them more quickly.
- Supernova: Launches a massive ball of energy that can be guided to some extent with the circle pad.
- Homing Missles: Launches a flurry of missiles that lock on and pursue any players in sight.
- Transposer: Upon activation the user will switch places with a nearby enemy, which can be used as a method of confusion or trapping.
- Stealth Mines: Releases multiple floating mines behind the Arwing. These mines stay invisible until in close proximity.
- Firebird: An extremely rare power-up. Upon activation the user's Arwing becomes engulfed in flames and inflicts instant death on anyone the user boosts into. Whilst this power-up is activated, the user's laser(s) are temporarily disabled.