Golden Sun is a contemporary presentation of the traditional console role-playing game formula, where the player guides a cast of four characters as they journey through a fantasy-themed game world, interact with other characters, battle many monsters, acquire increasingly powerful magic spells and equipment, and take part in a building, predefined narrative. While many actions the player takes are compulsory, Golden Sun often allows the player to complete certain objectives out of order, and to visit previous locations, which can advance minor story elements.

Much of the game's time spent outside of battle takes place in dungeons, caves, and other locales involving a lot of puzzles integrated into their layout. One must push logs into rivers in order to cross them, shift the track of a mine cart to access new areas, and a host of other activities in order to get from point A to point B and progress through the story and game world.