Radiant Historia is a traditional Japanese RPG which focuses on time travel. The story is set in a world torn by war and apparently facing imminent destruction. Stocke, the hero, is one of the finest secret agents of the Alistel nation. He, along with two other agents, is charged with a mission to escort a spy with valuable intel back into Alistel. Stocke also obtains a book from his superior called "The White Chronicle" which, as it soon turns out, allows him a small insight into the future and the ability to travel back in time. It is now that he must alter his past choices in order to save his comrades and make the history right.

The gameplay consists of a traditional, top-down view exploration part and a turn-based battle system. During fights, the enemies are placed on a 3x3 grid, on which they are free to move. The strategic element is to use skills which change their position giving you an advantage, since attacks work on all enemies occupying the same space and the player's characters sustain less damage when hit from the back rows. Players are also given the ability to switch a character's turn with that of the enemy/another character at the expense of being more vulnerable to getting hurt. This is used to boost the attack combo count - the higher combo the player achieves, the more damage he or she inflicts, gaining some additional experience after battle. During the exploration part the enemies are visible on the map, where the player can engage them by hitting with Stocke's sword, granting the party an advantage.

The story plays out in a semi-linear fashion. The player is free to replay previous events, changing choices and observing a new outcome. The game features multiple endings based on decisions made while traveling in time.