As the novel begins, Johnny Tremain, the fourteen-year-old main character, is both intelligent and gifted, yet he is also quite arrogant. Working as a silversmith's apprentice, he is seen as a leader by his fellow apprentices, who both admire and resent him. After a workplace accident leaves his hand crippled, Johnny must find a new way to support himself. He learns to ride a nervous horse named "Goblin" to secure a job delivering newspapers. As Johnny becomes an adept rider, he starts to come to terms with his disability. To manage Goblin, he must use his injured hand: "He could not keep it proudly in his pocket while careening about on a horse like Goblin." Johnny is the only character who undergoes significant change, learning humility through adversity and discovering his true strengths and weaknesses.

The other characters in the story remain static. Johnny's fellow apprentices at Mr. Lapham's silver shop—the lazy and spiteful Tory, Dove, and the somewhat clueless Dusty—do not change, even after leaving the shop. Despite their lack of development, these characters are crucial because Johnny's changing perceptions of and interactions with them highlight his growth. As Johnny matures, he makes more effort to understand others, becoming more considerate and tolerant of Dove and Dusty.

Two of Johnny's friends—Priscilla Lapham, one of the silversmith's daughters, and Rab Silsbee, a printer's apprentice—play significant roles in his development, even though they themselves change little. Priscilla, also known as Cilia, teaches Johnny about loyalty and love, especially when she defies her mother's orders to support Johnny during his theft trial. Rab imparts lessons on friendship and empathy. Although an adept fighter, Rab avoids conflict unless absolutely necessary. His compelling presence energizes those around him, and he becomes a role model for Johnny, who aspires to emulate Rab's leadership qualities.

Alongside the fictional characters, historical figures who led Boston's rebels appear in the story. Johnny meets Paul Revere, Samuel Adams, John Adams, James Otis, and John Hancock. Revere, also a silversmith, offers Johnny an apprenticeship before an accident shatters Johnny's chances of pursuing that career. After the accident, Johnny tries to secure a job at John Hancock's counting house. Although his injury prevents him from even writing Hancock's name, Hancock gives him a purse of silver coins despite not hiring him. As a rider for the Observers, a group focused on American independence, Johnny attends meetings with these historical figures. His interactions with these leaders and his contributions to their cause hint that America's independence was achieved through the bravery of unsung heroes.

Johnny Tremain explores themes of struggle and maturity. Just as Johnny strives to become an independent adult, the Boston Whigs fight for their land's independence. By the story's conclusion, Johnny has reached adulthood; a few years later, the colonists will have also won their independence.