The movie opens with Injun Joe (Eric Schweig) accepting a job position from Doctor Jonas Robinson (William Newman). Tom Sawyer (Jonathan Taylor Thomas) is then seen running away from home. He and his friends ride down the Mississippi River on a raft, but hit a sharp rock, which throws Tom into the water. His friends find him washed up on the shore, and Tom finds it was Huck Finn (Brad Renfro) who carried him to safety. Huck learns of an unusual way to remove warts - by taking a dead cat to the graveyard at night. There they witness Injun Joe and Muff Potter (Mike McShane), the town drunk, digging up the grave of Vic "One-Eyed" Murrell for Doctor Robinson. A treasure map is discovered and when Doc tries to betray the two men, Injun Joe murders him with Muff's knife.
The next morning, Muff is charged for the murder. Unfortunately, Tom and Huck had signed an oath saying that if either of them came forward about it, they would drop dead and rot. The boys embark on a search for Injun Joe's treasure map, so they can declare Muff innocent and still keep their oath. The only problem is, the map is in Injun Joe's pocket. After Injun Joe finds the last treasure, he burns the map, leaving no evidence to claim Muff innocent. Joe then discovers that Tom was a witness to the crime. He finds Tom and threatens he will kill him if he ever tells anyone about the murder. However, at the time, the entire community believed that he was dead, and the friendship between Tom and Huck starts to decline because of the fact that their evidence (the map) to prove Muff innocent, while preserving their oath, is destroyed.
At Muff Potter's trial, Tom decides that his friendship with Muff is more important than his oath with Huck and tells the truth. The court finds Muff innocent of all charges and goes after Injun Joe. As a result, Injun Joe decides to hold up his end of the bargain by killing Tom. When Injun Joe returns to the tavern, he kills his accomplice Emmett (Lanny Flaherty) for cheating him. Huck becomes angry with Tom for breaking their oath and leaves town. During a festival the next day, a group of children, including Tom and his love interest Becky Thatcher (Rachael Leigh Cook), enter the caves where Tom and Becky become lost. They stumble upon Injun Joe (who was looking for Tom) in McDougal's Cave. He traps them, but Tom and Becky manage to escape. Then they find the treasure and Tom tells Becky to go get her father and bring him back.
Just then, Injun Joe finds Tom, and again tries to kill him. But Huck returns to help save Tom, and battles Injun Joe. But Injun Joe easily overpowers Huck; just as he is about to kill him, Tom holds the treasure chest over a chasm. Injun Joe then tries to get the chest from Tom, only to fall into the chasm to his death (with the chest which was empty). The boys reconcile, and are declared heroes by the people. Tom is praised on the front page of the newspaper, and Widow Douglas (Marian Seldes) decides to adopt Huck Finn.
- Jonathan Taylor Thomas as Thomas "Tom" Sawyer
- Brad Renfro as Huckleberry "Huck" Finn
- Eric Schweig as Injun Joe
- Charles Rocket as Judge Thatcher
- Amy Wright as Aunt Polly
- Mike McShane as Muff Potter
- Marian Seldes as Widow Douglas
- Rachael Leigh Cook as Rebecca "Becky" Thatcher
- Courtland Mead as Cousin Sid
- Joey Stinson as Joseph "Joe" Harper
- Blake Heron as Benjamin "Ben" Rodgers
- Lanny Flaherty as Emmett: Injun Joe's accomplice.
- Peter MacKenzie as Mr. Sneed
- Heath Lamberts as Mr. Dobbins
- William Newman as Doctor Jonas Robinson
- Andy Stahl as Sheriff
- Bronwen Murray as Cousin Mary