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.

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 Japanese release, Edward and Golbez are named Gilbert and Golbeza. This was changed when being brought over to the US due to playable characters only being able to have 6 letters in their name.

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.