When the novel opens, Johnny Tremain, the fourteen-year-old protagonist, is intelligent and talented but also arrogant. A silversmith's apprentice, he is perceived as a leader by the other apprentices, who both resent and admire him. After an accident at work cripples his hand, he must find another means of supporting himself. He develops new skills, learning to ride a skittish horse, "Goblin," in order to get a job delivering newspapers. As Johnny becomes a skilled rider, he begins to accept his disability. To keep Goblin under control, he must use his crippled hand: "He could not keep it proudly in his pocket while careening about on a horse like Goblin." The only character in the story who changes, Johnny learns humility as through adversity and struggle he discovers his true strengths and weaknesses.

The secondary characters remain unchanged throughout the story. Johnny's fellow apprentices at Mr. Lapham's silver shop—the lazy, vindictive Tory, Dove, and the somewhat dimwitted Dusty—stay the same, even after they leave the silver shop. These characters are important, however, because the changes in Johnny's perceptions of and reactions to them indicate his development. As he matures, Johnny makes a greater effort to understand others and becomes kinder and more tolerant toward Dove and Dusty.

Two of Johnny's friends—Priscilla Lapham, one of the silversmith's daughters, and Rab Silsbee, a printer's apprentice—contribute significantly to his development, though they do not change much themselves. Priscilla, known as Cilia, teaches him the meaning of loyalty and love, especially when she defies her mother's orders and comes to help Johnny when he is tried for theft. Rab teaches him about friendship and sensitivity. An accomplished fighter, Rab nonetheless avoids fights unless absolutely necessary. Rab's riveting presence invigorates everyone around him. He becomes a role model for Johnny, who tries to emulate the older boy's leadership qualities.

In addition to the fictional characters, historical figures who led Boston's rebels also appear in the narrative. Johnny encounters Paul Revere, Samuel Adams, John Adams, James Otis, and John Hancock. Revere, a silversmith, offers Johnny an apprenticeship in his shop before Johnny's accident ruins his chances of becoming a silversmith, and Johnny tries to get a job in John Hancock's counting house after the accident. Johnny's injury renders him incapable of even writing Hancock's name, but Hancock gives him a purse full of silver coins after refusing to hire him. As a rider for the Observers, a group working toward American independence, Johnny has the opportunity to join the meetings of these historical characters. Johnny's interactions with these famous figures and his important contributions to their efforts suggest that America gained independence because of the courage of anonymous heroes.

Johnny Tremain deals with the themes of struggle and maturity. Just as Johnny strives to become an independent adult, the Boston Whigs struggle to win independence for their land. At the end of the narrative, Johnny reaches adulthood; several years later, the colonists, too, will have earned their independence.