In all versions of the game there is a secret passage in Cafe HOWDY!/Pub Lali-Ho in the Dwarven Castle of the Underworld that leads to a place called the "Developer's Room". In it are recolored sprites that are meant to be the developers of the game. In the DS release, it has the developers of the DS remake instead. This area was cut in "Final Fantasy 4 Easy-Type" and "Final Fantasy 2 (US)" because it's possible to find a pornographic magazine in the room, called Lustful Lali-Ho.

The final boss, Zeromus, had a complete redesign for Final Fantasy 4 Easy Type. He was also made a lot harder, such as using Big Bang at the start of the battle. Zeromus EG in the Game Boy Advance and PlayStation Portable version is based on this version.

Originally, the translated script of the DS version of IV was simply going to copy and paste the English script of the Game Boy Advance version with some alterations. Translator Tom Slattery, however, was a huge fan of the original game and offered to translate the entire game from scratch, making it more accurate to the original Japanese text while also using some modern series terms (such as "Eidolons" for the summon monsters.)

The Game Boy Advance version of Final Fantasy IV contains the line “I’ll bet you and your goons wrecked them up something awful.” This is a reference to the Something Awful forums, a popular site in the 2000s, whose members are collectively referred to as goons.