Magi-Nation for Game Boy Advance was released only in Japan on December 12, 2002, as a remake of the Magi-Nation for Game Boy Color. In addition to featuring visual upgrades, including sprites, the main character was redesigned as Dan Monma.

Dan Monma, a resident of Yokohara Town, finds himself in the Moonlands after being dared to enter a cave. Hailed as the prophesied savior of the Moonlands, Gia sends Dan with the Core Glyph to seal Agram's Shadow Geysers by retrieving the Core Stones. To do so, Dan must defeat Agram's henchmen within the five Moonlands of Naroom, the Underneath, Cald, Orothe, and Arderial. After placing the five Core Stones in the Core Glyph, Dan now must face off against Agram. After defeating Agram and saving the Elivan race, Dan returns home to Earth.

In addition to the Creatures available in Magi-Nation (GBC), five Dream Creatures were made forgeable which were unforgeable in the GBC version: Platheus, Sphor, Xyx, Thunder Hyren, and Bolt Hyren. Likewise, several Dream Creatures were replaced:

-Core Grag → Darkbreed Hyren
-Hook Wing → Chaos Plith
-Jingjack → Gorath
-Kazor → Dark Furok
-Kletch → Grubble
-Leaf Chogo → Balamant
-Sarbil → Tragan
-Spindle → Szalak
-Vile Yogu → Harban
-Yvohcna → Drush