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.

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

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.

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

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.

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.

If the player talks to the trumpet player in Onett, he will play "Symphony No.9 Movement 2" composed by Antonin Dvorak.

The four major cities in EagleLand are all named after numbers: Onett, Twoson, Threed and Fourside.

There are two arcade cabinets found only in the Onett Arcade, which show recognizable screens of the Donkey Kong and Space Invaders arcade games.

If there is second controller connected, it's possible to control the game with both controllers.

Using the Pencil eraser on Ness's Nightmare outside of battle, a dialogue box will say, "Do you really think this look likes a pencil?". Using the Eraser eraser says, "It looks like some sort of primitive human statue if you look at it from the right angle... But it definitely doesn't look like an eraser... does it?"

The last scene of the game's opening cinematic features Ness approaching Giant Step, alone, at nighttime. However, this is impossible to do in the actual game. The only two times that Spoiler:Onett (the town where Giant Step is located) can be explored at night time are at the meteor crash, the search for Picky at the very beginning of the game, and Spoiler:Giygas's last-minute invasion of Onett near the end of the game. During the former, Spoiler:Ness cannot obtain the key to the Shack, which is required to access Giant Step. During the latter, Spoiler:Ness has a full party of four, meaning that he cannot access Giant Step on his own.

Storing a damaged Teddy Bear with the Escargo Express or Tracy after it is damaged, and then checking it out again will restore it to full health.

Unused miniature sprites of what appear to be the Photo-Man and an Escargo Express delivery man can be found within the game's code, suggesting that they may have appeared in the Lost Underground at some point during development.

Paula's Theme is a remix of the theme of Youngtown from the original Mother.

The fetch and progress system in the Monkey Cave is similar to that of the "Beneath the Well" mini-dungeon from The Legend of Zelda: Majora's Mask. It's possible that Nintendo was referencing this system in Majora's Mask.

Some fans have theorized that Jeff's father, Dr. Andonuts, is actually Loid from the original Mother grown up. This can be evidenced by thier similar hair color, glasses, and the fact that they both hide in garbage cans when frightened. It's also important to note that both Loid and Jeff can use bottle rockets as weapons during battle.

At the 3rd "Your Sanctuary" location, Milky Well, if there is either a dead or diamondized party member, there will be a typo saying "The power of Milkey Well flowed into [Party Member's Name]."

The director for the United States localization needed a name for Porky's father so he named him "Aloysius," a reference to Looney Tunes where Daffy Duck gives the name to a giant to save himself from being giant food, because he thought the name was "dumb and funny."

By plugging in a second controller and pressing Select during the cutscene where Ness, Porky and Picky encounter the Meteorite and Buzz Buzz, the direction and length of the light that shines from it can be changed. The height in which the cutscene is activated seems to affect how the light behaves, and it seems to be intrinsically linked to where Buzz Buzz's sprite moves on-screen as the light will sometimes follow his looping animation by extending or retracting slightly.