Set in the Suikoden universe, the game closely follows the story of Suikoden II. The hero is a young member of the Unicorn Brigade of the Highland Army. One night, your camp is attacked. You and your best friend Jowy escape, and the fate takes you into different directions, when you get involved in a war between several nations.

Unlike the main Suikoden games, Gensou Suikoden Card Stories is a card-based RPG. Most of the game is spent playing a special card game with your opponents. The complex card game is not unlike a strategy battle: you have three types of cards, some of which take you to a specific "mission" (you open the game with such cards), while others represent various characters with different strengths and weaknesses. You can acquire cards in shops, get them from your opponents, and also look for them in randomly generated dungeons.