The J2ME version of FIFA 2006 adapts the game to an isometric version, similar to the pre-FIFA 97 releases. Although the game is fully-licensed, it does not have the extensive amount of teams and players the console versions offer. Only national teams are available and there are no leagues with specific clubs.

The game improves over the 2005 edition with new gameplay modes, a few cutscenes, and more teams to choose from. The main game modes are Tutorial, Quick Match, Friendly, Cup, Scenario and Shoot Out. The new Scenario mode offers specific tasks at the end of a season, such as finishing first in a league, finishing above a red line to keep the fans loyal, or saving a team from relegation.

Before each match, you can define the line-up, formation and strategy. During the game, you can introduce substitutions or view statistics. While playing, the players can be controlled in eight directions, and there are keys to pass, change the active player, tackle, and shoot. The amount of time you keep a key pressed defines the power, length, of the type of shot. This allows for specific moves such as lobs, cross passes, headers, through passes and clearance kicks.

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