If you use Shinespark to rush through a difficult area of Sector 4, dialogue involving Samus interrupting a conversation between Adam and a mysterious figure implied to be from the Galactic Federation will roll, ending with Adam remarking "I wonder how many players will see this message...?"

The short jingle titled "Objective Complete" that plays at certain points throughout the game sounds nearly identical to the "Race Start" jingle from F-Zero.

In the beginning of the game, in Sector 1, X parasites have infested 5 atmospheric stabilizers and you have to restore them to normal. Look closely at these atmospheric stabilizers and you will see a hidden GameCube console in the top-left corner.

In the Chozo language, the word "Metroid" roughly translates to mean "ultimate warrior."

It is possible this name was chosen because the Chozo created the Metroids to fight the highly dangerous X parasite on SR388.

There are a few inconsistencies between the appearance of the Omega Metroids in Metroid II: Return of Samus and the one at the end of Metroid Fusion. The first is the size of it, as it was 150% Samus' size in Metroid II, but is now twice her size. This could be linked to the baby Metroid in Super Metroid, who grew larger late into the game. Another inconsistency is the fact that it's only weakness in Metroid Fusion is the Ice Beam, when the Ice Beam had no effect in Metroid II.

When completing Normal Mode in the Japanese version, the player is given different ending images. These images (with the exception of the last) feature Samus without her suit and show her Chozo upbringing and parent's death. The artwork heavily adheres to the events depicted in the Metroid Manga, written by Kouji Tazawa and advised by Metroid director Yoshio Sakamoto.

Metroid Fusion is one of only a few Game Boy Advance games to have a save battery through an SRAM chip in its cartridge, though this would only appear in earlier-produced carts, as the SRAM chip was scrapped from use halfway through production in favor of a battery-free EPROM chip.

According to a 2003 interview with the game's director/writer Yoshio Sakamoto published in GSLA, he stated that after Super Metroid on the Super Famicom, they couldn't use the underpowered Game Boy Color for a new Metroid game. When the Game Boy Advance was released, a console whose specs surpassed the Super Famicom, the team from the mobile games division really wanted to work with it.

Due to a glitch, Samus' left wall jump sprites in-game do not have her left arm. This is due to a rendering error, as internally these sprites do have her left arm. This does not happen with her right wall jump sprites.