A debug menu is available within the game's code, and can be accessed through the use of a cheat device. The menu's cursor is a sprite of Kirby from Kirby's Dream Course, which was originally released a month after EarthBound in Japan.

In the Dusty Dunes Desert there is a lone white pixel and a lone black pixel. Talking to them will reveal that they are talking sesame seeds that wish to be together. Other than longing for each other, they serve no other purpose than being notoriously difficult to find.

Shigesato Itoi revealed in a 2003 interview that Tony, Jeff's roommate at the Snow Wood Boarding House in Winters, is homosexual:

Before the final battle, Spoiler:Pokey's second-to-last line reads, "Master Giygas - No, Giygas is no longer the wielder of Evil." In the original Japanese version, Pokey consistently referred to Giygas as "Master Giygas" until this point, where he discards the title as a sign of disrespect.

This line was carried over from the Japanese version, but Pokey usually just calls him "Giygas" throughout the English version, and so the context was lost.

Three of the songs in the game are each composed entirely of a single sample played at various pitches.
• Cave of the Past - "Deirdre" by The Beach Boys
• Moonside - "Keep on Laughin'" by Ric Ocacek
• Cave of the Present - "All You Need Is Love" by The Beatles

There are four unused sprites of King, which show him climbing a ladder or rope. This would suggest two things: either King was supposed to remain in the party longer, or Ness' original travels through Onett were supposed to include something to climb.

In the Japanese version, the intro says, "Gyiyg Strikes Back!", but was changed in the International release to, "The War Against Giygas!". This could've been possibly an overly-cautious attempt to avoid conflict with Lucasfilm over The Empire Strikes Back.

Most drug stores became shops in the North American version, although the one in Dusty Dunes Desert still has a prominent "Drug" sign in front of it.

Early previews of EarthBound show that the game's localizers had considered calling Giygas "The Geek".

Shigesato Itoi personally wrote every line of the script in Mother 2 (besides Moonside) to give the characters more personality.

In the September 1994 issue of Weekly Famitsu, Shigesato Itoi stated that the rolling health meter in battle was originally going to be made of Pachinko beads. The idea came to him when a Pachinko parlor opened right by their office. He thought that the idea would be scary to see a stream of beads rattling out from Ness and his friends. However, it was difficult for them to portray it on screen, as when the amount increased, it covered up 1/3 of the screen.

In the issue of Weekly Famitsu published in 9th of September 1994, Itoi refers to the battle backgrounds as a "Video Relaxant." The Video Relaxant was going to be an in-game item and was originally referred to as a "Video Drug". It can still be found in the game's files. It has no function and the description of the item is "What the hey is this?"

Giygas' weakest form has an outline of a Fetus hidden in it.

An unused sprite of Mr. Everdred as a ghost is present in the game's ROM. It is assumed that either he was going to be a party member at one point during development (when one of the party members faints, they will appear as a ghost) or Spoiler:when Mr. Everdred was beaten near Jackie's Cafe in Fourside, a ghost would have flown out of his body. Its true purpose has never been confirmed.

The official strategy guide included with all copies of the game contains several errors. For example, it claims that the Kraken enemies in the Sea of Eden drop the Gutsy Bat item. The item is actually found in the Cave of the Past area, dropped by the Bionic Kraken enemy.

At the time of EarthBound's development, Shigesato Itoi didn't know how to use computers. He would actually speak each line of dialogue out loud, often one letter at a time, and Matchan Miura typed it up. Itoi used Miura's reactions as a gauge of how good a line was.

The "Casey Bat" is the reward for beating Master Puke. This bat is a reference to the old poem "Casey at the Bat" and, as can be expected based on the poem, is very strong but almost never successfully hits enemies.

In the official strategy guide for EarthBound, there are pages about the town's attractions, accompanied by fun facts, such as:
• Onett Has a population of 3,500 people and 2 dogs.
• Twoson has 10 vendors in the park and 15 mushrooms.
• In Threed, there are 2 Graveyards, 2,000 zombies, and a grand total of 0 lions, tigers, and bears.
• In Dusty Dunes Desert, there are 2,000,001 Cacti, and 5 people living there.
• There is an average of 0 Temper Tantrums in Dalaam.
• Deep Darkness has 4,000,603 Mosquitos.

EarthBound features five types of anti-piracy:

• First, it will simply check to make sure the cartridge isn't being used in a PAL console.
• Second, it will perform two SRAM checks at startup.
• Third, if the first two measures are disabled, the enemies on screen will be ramped up to ridiculous levels and you will find enemies in areas they don't belong in.
• Fourth, there's another SRAM checker that is called up six times during the game. Its purpose is unknown as of yet.
• Fifth and finally, if the game detects problems after Pokey turns off the Devil's Machine, the game will erase all of your save data and freeze, forcing you to go back to reset and find all of your work gone.

During a livestream of the game with EarthBound Central, Marcus Lindblot revealed a couple secrets of the game's localization. For example, the character of Nico from Magicant was based on Marcus' real-life daughter, who was born while he was working on the game. Nobody had known where the name Nico came from prior to this, as the character didn't have that name in the Japanese version.