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.

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.)

Edward is seen with a lute in Yoshitaka Amano's artwork and in the opening cinematic in the Final Fantasy IV DS remake, while in the game itself he plays a harp.

According to executive producer Takashi Tokita (scenario writer of the original release), 3/4 of the original script had been cut from the Super Nintendo release due to hardware limitations, but some of this lost material was reworked into the DS remake.

In the iOS port of the game, Cecil is introduced as "Load Captain Baron Red Wings" instead of "Lord Captain". This error is fixed in later releases of the game.

In the final battle against Zeromus, Edge can steal an item known as Dark Matter in the Japanese version of Final Fantasy 4. This item, long thought to reduce the damage of Zeromus's Big Bang attack, is actually a joke item. In the DS version, a superboss named Proto-Babil appears if you use this item on the face of the Moon.