Tom Sawyer is a fun-loving orphan who lives with his aunt Polly, her daughter Mary, and his half-brother Sid in St. Petersburg, Missouri, during the 1840s. He is a rebellious youngster who often sneaks jam from the pantry, gets into fights, and skips school to go swimming instead. One Friday night, Aunt Polly discovers her mischievous nephew coming home late and deduces that he has been in a fight. She gets exasperated and makes him whitewash her fence the next day. However, Tom is a master of reverse psychology and a charismatic salesperson, so he convinces several neighborhood kids to trade their personal items in exchange for the "privilege" of doing his "fun" work for him. By the time he is done with his scam, Aunt Polly is amazed to see that the fence has three coats of paint on it. Tom then falls in love with the new girl in town, Becky Thatcher. He tries to win her affection by hanging around her house, but when a maid throws some water outside the Thatcher residence, Tom gets drenched instead.
On Sunday, Tom struggles to memorize Bible verses for Sunday school. Ever the enterprising salesperson, he trades the items that he previously acquired on Saturday for tickets that are normally awarded for memorizing Bible verses. Tom’s plan is to collect enough tickets from his friends so that he can be awarded a new Bible. Judge Thatcher arrives at the church, and he is accompanied by his daughter Becky, Tom’s current crush. Tom wins the Bible and earns respect from his friends and the adults who are present. However, he is soon humiliated when he is stumped by a simple question from Judge Thatcher about Jesus’s first disciples. Later, Tom is up to his usual mischief once again by disrupting a church service with his pet beetle. On Monday, Tom tries to skip school by pretending to have a sore tooth, but Aunt Polly cleverly sees through his charade and gets the loose tooth pulled out. Tom then makes plans with Huckleberry Finn, the son of the town drunkard, to go to the local cemetery that night. This makes Tom late for school, and he is punished by being made to sit with the girls. This actually does Tom a favor because he gets to sit with Becky Thatcher, his crush, and he confesses his love for her. They later share a kiss, but Tom upsets her by revealing that he had previously been engaged to a girl called Amy Lawrence. Tom considers running away and leading a pirate's life after Becky shuns him. He plays outlaw games with his friend, Joe Harper, before joining Huckleberry Finn for their secret rendezvous at the cemetery. At the cemetery, Huck and Tom witness three grave robbers, Dr. Robinson, Injun Joe, and Muff Potter, having a heated quarrel. Robinson knocks out Potter, who is drunk, but then Injun Joe stabs Robinson to death with Potter’s knife and later claims that Potter committed the murder. The boys are too scared to come forward with their eyewitness accounts of the actual truth, and they take an oath not to tell anyone about the incident. The next day, Potter is imprisoned based on Injun Joe’s testimony and awaits trial. Tom starts to feel guilty, and Becky’s lack of interest in him makes Tom even more depressed. He hatches a plan to run away with his friends Joe Harper and Huckleberry Finn, and the boys sail away on a raft to Jackson’s Island to live like outlaws. They spend the day on the island, but then spot the townsfolk searching for their bodies on the river, believing that they have drowned. Tom later sneaks back into town and eavesdrops on his sad family members as they reminisce about the missing boys, who are now presumed dead. After Tom returns to the island, the boys soon grow homesick after a period of fun and games and learning how to smoke. Tom convinces them to reappear back in town on the day of their funeral. When the boys show up as planned, they are welcomed back with joy. Aunt Polly dotes on Tom that week, and even Becky tries to win his affection, but Tom ignores her and spends time with Amy Lawrence instead.
Tom and Becky later mend their relationship when Tom takes the blame for Becky tearing an anatomy textbook in class. School ends for the summer, and Tom catches a bad bout of measles. Later, at Muff Potter’s trial, Tom testifies against Injun Joe, saying that he was the real killer. Injun Joe manages to escape, and Tom is hailed as a hero for saving an innocent man from jail. That summer, Huck and Tom go hunting for buried treasure, and they start frequenting an abandoned house that is rumored to be haunted. However, the boys later spot Injun Joe there—he and an accomplice have arrived to hide some money they stole. Much to the boy’s amazement, the criminals find a chest of gold coins in the process of hiding their money. Injun Joe spots the boys’ shovels in the house and gets spooked, realizing that other people might be visiting the house—he decides to take his loot elsewhere. Tom becomes obsessed with finding Injun Joe’s hiding place for the treasure and enlists Huck to shadow the criminal and his accomplice everywhere. One night, Huck follows them to Widow Douglas’s house and learns that the crooks plan to kill her because her husband once whipped Injun Joe for vagrancy. Huck, who has a soft spot for the kind widow, immediately summons her neighbor, the Welshman, who scares Injun Joe and his friend away. Huck falls sick at the Welshman’s house, and Widow Douglas takes care of him. Meanwhile, Tom and Becky go to explore MacDougal's Cave. They soon get lost in the labyrinthine tunnels, and the townsfolk start searching for them when they do not return. While searching for a way out, Tom suddenly spots Injun Joe in one of the tunnels, and the criminal runs away. Tom and Becky finally escape the cave after Tom’s persistent efforts to find a way out bear fruit. After recovering from his ordeal, Tom learns that Huck had fallen sick and that Injun Joe’s accomplice had drowned. Tom realizes that Injun Joe must be still in MacDougal's Cave after learning that Judge Thatcher had sealed the entrance shut. Sure enough, Injun Joe was later found dead there. Suspecting that the treasure must be nearby, Tom and Huck go searching for it in MacDougal's Cave. They finally find the treasure, much to the surprise and acclaim of the townsfolk, and the 12 thousand dollars they retrieved are invested on their behalf. Judge Thatcher approves of Tom’s intelligence and sees him as a future lawyer. Widow Douglas decides to adopt Huck, but he soon tires of civilized life and tries to run away. He finally agrees to stay with the widow after Tom promises that the free-spirited Huck can be a part of his gang.