Before Yoshitaka Amano drew the final artwork, Sabin, Edgar and their backstory were designed by Kaori Tanaka (later nicknamed Soraya Saga), an artist who would go on to participate in the development of Xenogears. Two royal siblings named Rene and Roni appear in the latter game. Soraya Saga also authored the doujinshi (a term for a fan made manga), Figaro no Kekkon: Tales from Desert, which explores Sabin and Edgar's backstory.

Umaro was originally supposed to be a random encounter on the world map and could only be caught with bait. Hidden game data suggests Umaro was at some point intended to be able to be encountered in the World of Balance, as an unused battle complete with stats and a simple AI script exists within the game's data.

According to Hironobu Sakaguchi, Umaro has a strong sense of honor and feels like he owes a debt to Mog, because Mog shared some food with him when he had collapsed from exhaustion.

During development, Strago had a 65-year-old wife named Lara. They had amusing arguments with each other claiming the other will die first, but she was ultimately cut from the game. In the game's original strategy guide, Strago and Relm are said to fight with stuffed toys. This might be another idea that was tossed around during development, but in the end was never implemented. The idea wasn't used until Final Fantasy X, in which the character Lulu uses stuffed toys as weapons.

Real life professional wrestler and world champion Joshua Harter wrestles under the ring name "Chris Sabin", a direct reference to Sabin Figaro.

Terra's name in the Japanese version is "Tina". Her name was changed because most of the playtesters hated it, and because it was a common name in the US. Because the game allows the player to rename the characters, and the player might name one of them after themselves, the localization team wanted to avoid using common western names for any of the characters.

Gau's name is a pun. The word "gao" is the Japanese onomatopoeia for an animal's growl or roar. The joke was that Gau would "roar" at the party when they asked him his name, unless the player had decided to change Gau's name.

This joke was lost in the English translation: Gau would always respond to the party's inquiry with a "roar", no matter what his name was set as.

Celes was originally meant to be a "conflicted spy" archetype - a spy working for the antagonists, but swayed by the benevolence of the people she was supposed to be spying on, and how nice Locke was to her. She was to be psychologically unstable, like Kefka, due to a similar magic infusion process. Although the "conflicted spy" idea was not used in the final game, the archetype was used for Cait Sith in Final Fantasy VII. Celes was Yoshinori Kitase's favorite Final Fantasy VI character from a developer's point of view. Kitase has stated that at first, Celes did not have as much of a role but this changed later in development.

Parts of Cyan's story were supposed to involve an extra character named Angela who was eventually cut from the game. She was a "big sister" archetype and had a take-charge, sultry attitude. She would often flirt with Cyan, who, considering his personality, would always overreact to her. It is unknown if she was an NPC or playable character, but she was probably planned to be playable as she had a whip as a weapon.

It was originally intended for Gogo to be found in any of the bars in the World of Ruin disguised as one of the player characters not in the player's active party. Gogo would randomly cycle between the towns based on a timer and if the player managed to speak to him/her with the real character s/he was disguised as, Gogo would reveal him/herself and join the party.

The developers felt the quest was too difficult and changed this for the final version of the game. This could possibly suggest that the Siegfried/Ziegfried imposter was meant to be Gogo during development.

In the Japanese version of FF6, Setzer joins the party with a Bandana equipped, even though he cannot equip bandanas (if the Bandana is removed, he cannot re-equip it). This is not a bug, but was meant to be an inside joke showing Setzer's vanity does not allow him to wear the same things as Locke. In the GBA version Setzer does not come with a Bandana, as the porting team possibly thought it was a glitch.

If the player speaks to the Figaro merchants while Edgar is the party leader, they will receive a 50% discount on all purchases.

According to an interview with Nobuo Uematsu, the composer of most Final Fantasy games, the music from Final Fantasy VI was Uematsu's favorite score. Final Fantasy VI was also Uematsu's favorite game to play.

When the Chainsaw weapon's instant death attack is used, Edgar and Gogo don a hockey goalie's mask in a similar fashion to Jason Voorhees from Friday the 13th.

The original Japanese name of the esper 'Crusader' was 'Jihad'. It was renamed due to censorship.

The playable characters of Shadow and Relm are father and daughter. Never stated directly in game, it is told through flashbacks when you sleep at an inn with Shadow in the party. Later, in 1998 a developer confirmed this in an interview, saying that the scene was to go as follows:

The final battle Spoiler:with Kefka references Dante Alighieri's Divine Comedy. Spoiler:The battle starts with a devil like creature (Hell), then goes on to a level with a number of people (Purgatory, where the souls wait to be judged). Then the party does battle with creatures that look like Michelangelo's Pietà  (a sculpture of Jesus lying in Mary's lap after he was crucified). The battle concludes with a Kefka's angel in heaven. In the story, Dante asked God what the meaning of life was. This is mirrored by Kafka telling the heroes that "life is meaningless." It is also possible that Kefka is referencing Lucifer, who is known as a fallen angel. One of his attacks is called 'Fallen One,' which is one of the titles of Lucifer.

It's possible to play as General Leo in places you weren't meant to. Using the airship glitch (which is done by first getting the airship, flying around, getting back to the floating continent, saving, and then dying, giving you use of the airship to travel to any part of the world) you can skip getting a majority of the characters besides a select few. These character's slots will be replaced by characters only used in certain parts of the game, like General Leo.

There are multiple examples of art assets being censored in the North American release.
Esper Siren, Esper Starlet, Alluring Rider, Madam, The Goddess and Chadarnook's Godess part were all altered to be more acceptable to international audiences, mostly covering up more skin, or in Madam's case, removing smoking references.
Additionally, the Cafe sign originally read "Pub".
Many of these changes were kept in place in the Game Boy Advance port of the game.

There are three unused enemies hidden in the game's code. These are CzarDragon, Colossus and an alternate Umaro. The Colossus and Umaro use the same graphics and palettes as other enemies in the game. The Colossus is fairly simple and has a full attack script, and the alternate Umaro is weaker than the original.

CzarDragon however has no script, so when the battle begins, all it does is attack repeatedly. Which is odd, as there's a line of battle dialogue for the enemy, as though it was intended to be fought. The dialogue reads:
Mwa, ha ha... Humans and their desires! I'm free at last! I bring you destruction... I bring you terror... I am Czar... Prepare yourselves!
Taking into account the dialogue and its likeness to Shinryu in Final Fantasy V, it seems as though CzarDragon was intended to be an optional end boss. In the Gameboy Advance rerelease, CzarDragon can be fought under its original Japanese name Kaiser Dragon. It has a unique sprite similar to the SNES design.

In a 1994 Hippon Super and Game-on magazines interview, the game's field graphics designer Tomoe Inazawa wanted the Serpent Trench's ocean floor less shallow-looking by making it darker and more impenetrable, realistic and alluring than how the ocean appeared in previous Final Fantasy games:

"Well, in reality, that’s how the ocean floor is: dark and impenetrable. What has been depicted in earlier games is really a shallower image of the ocean. So I was thinking about how to convey something more realistic, so I made it dark. Dark and alluring."