Orphan Tom Sawyer lives with his Aunt Polly and his half-brother Sid in the town of St. Petersburg, Missouri, sometime in the 1840s. He frequently skips school to play or go swimming. When Polly catches him sneaking home late on a Friday evening and discovers that he has been in a fight, she makes him whitewash her fence the next day as punishment.
Tom persuades several neighborhood children to trade him small trinkets and treasures for the "privilege" of doing his work, using reverse psychology to convince them of its enjoyable nature. Later, Tom trades the trinkets with students in his Sunday school class for tickets, given out for memorizing verses of Scripture. He collects enough tickets to earn a prized Bible from the teacher, despite being one of the worst students in the class and knowing almost nothing of Scripture, eliciting envy from the students and a mixture of pride and shock from the adults.
Tom falls in love with Becky Thatcher, a girl who is new in town. Tom wins the admiration of her father, the prominent Judge Thatcher, in the church by obtaining the Bible as a prize, but reveals his ignorance when he cannot answer basic questions about Scripture. Tom pursues Becky, eventually persuading her to get "engaged" by kissing her. Their romance soon collapses when she discovers that Tom was "engaged" to another schoolgirl, Amy Lawrence.
Becky spurns Tom, who accompanies Huckleberry Finn, a vagrant boy whom all the other boys admire, to a graveyard at midnight to perform a ritual intended to heal warts. At the graveyard, they witness three body snatchers, Dr. Robinson, Muff Potter and Injun Joe, robbing a grave. A fight breaks out, during which Robinson knocks Potter unconscious and is then murdered by Injun Joe. When Potter wakes up, Injun Joe puts the weapon in his hand and tells him that he killed Robinson while drunk. Tom and Huck swear a blood oath not to tell anyone about the murder, fearing that Injun Joe will find out and kill them for revenge. Potter is arrested and jailed to await trial, not disputing Injun Joe's claim.
Tom grows bored with school, and he, his friend/classmate Joe Harper, and Huck run away to Jackson's Island in the Mississippi River to begin life as "pirates". While enjoying their freedom, they notice the community is scouring the river for their bodies, as the boys are missing and presumed dead. Tom sneaks back home one night to observe the commotion and, after a moment of remorse at his loved ones' suffering, conceives a plan to attend his own funeral. The three carry out this scheme, appearing at church in the middle of their joint funeral service and winning the respect of their classmates for the stunt. Back in school, Becky rips a page in the school master's anatomy book after Tom startles her, but Tom regains her admiration by claiming responsibility for the damage and accepting the punishment that would have been hers.
During Potter's murder trial, Tom breaks his oath with Huck and testifies for the defense, identifying Injun Joe as the actual culprit. Injun Joe flees the courtroom before he can be apprehended; Potter is acquitted, but Tom and Huck now live in fear for their lives.
Once school lets out for the summer, Tom and Huck decide to hunt for buried treasure in the area. While investigating an abandoned house, they are interrupted by the arrival of two men; one of them is a Spaniard, supposedly deaf-mute, who is actually Injun Joe in disguise. He and his partner plan to bury some stolen treasure in the house, but inadvertently discover a hoard of gold coins while doing so. They decide to move it to a new hiding place, which Tom and Huck are determined to find. One night, Huck follows the men, who plan to break into the home of the wealthy Widow Douglas so Injun Joe can mutilate her face in revenge for being publicly whipped for vagrancy − a punishment handed down by her late husband, a justice of the peace. Huck summons help and prevents the break-in, but asks that his name not be made public for fear of retaliation by Injun Joe.
Shortly before Huck stops the crime, Tom goes on a picnic to a local cave with Becky and their classmates. Tom and Becky become lost and wander in the cave for days, facing starvation and dehydration. Becky becomes dehydrated and weak, and Tom's search for a way out grows more desperate. He encounters Injun Joe by chance, but is not seen. He eventually finds an exit, and he and Becky are joyfully welcomed back to town, learning that they have been missing for three days and traveled five miles from the entrance. Judge Thatcher has the cave's entrance door reinforced and locked. When Tom hears of this action two weeks later, he is horror-stricken, knowing that Injun Joe is still inside. He directs a posse to the cave, where they find Injun Joe dead of starvation just inside the entrance.
A week later, having deduced from Injun Joe's presence that the stolen gold must be hidden in the cave, Tom takes Huck there in search of it. They find the gold, which totals over $12,000 (equivalent to $392,000 in 2023) and is invested on their behalf. The Widow Douglas adopts Huck, who finds the restrictions of a civilized home life painful, attempting to escape back to his vagrant life. He reluctantly returns to the widow, persuaded by Tom's offer to form a high-class robber gang.
