In 1855, Tom Sawyer and his friends are growing up in the town of St. Petersburg, Missouri in the United States. Being wild children, Tom Sawyer and his best friend Huckleberry Finn are always getting into new adventures and one kind of trouble or another. So it's not entirely unexpected one day when Tom Sawyer heads off to school and realizes he is late...

Square no Tom Sawyer is a side-scrolling RPG that features characters and situations from Mark Twain's Tom Sawyer novels. Players control Tom himself and up to three other characters who can join his party at any one time. In town, there are a variety of people that can be talked to and shops where items can be bought and sold. Outside of towns, monsters and fierce woodland animals are randomly encountered and must be battled with.

When entering battle mode, the game shifts to a third-person view behind Tom's party. The player can issue commands such as Fight, Item, and Run to each of the characters in the party and these actions will occur in turn. Battles that are won earn the participating characters experience points. These experience points can be allocated to increase specific stats of characters. Players can accumulate new items for use in battle but never have to deal with equipping characters.