The True Confessions of Charlotte Doyle is a children's novel that follows the adventures of thirteen-year-old Charlotte Doyle as she immigrates from Liverpool, England to Providence, Rhode Island. As the only passenger on board the ship, Charlotte's voyage is disrupted when tensions among the crew result in her serving as a sailor. Though at times her new life is dangerous, Charlotte's experiences show her an inner strength she never knew she had, and a kind of life she never knew was possible.
The story starts in the early summer of 1832, as thirteen-year-old Charlotte Doyle prepares to take a big voyage from Liverpool, England to her family's new home in Providence, Rhode Island. Her upper class upbringing and her education in the very proper Barrington School for Better Girls gives her a very sheltered and narrow view of life. Charlotte finds herself the only passenger and the only female on the ship, the Seahawk , as the other two families coming with her don't arrive. Repeatedly, people tell her she shouldn't be on the ship, but her escort, Mr. Grummage, insists. Mr. Grummage rushes her, saying that her father wants her on the ship.
On her first day aboard, a black sailor named Zachariah gives her a dirk for protection. He also tells Charlotte a story about what Captain Jaggery did to a crewman's arm after he couldn't tie a good knot. Blinded by her view of the captain as a gentleman, she disbelieves him. The captain and Charlotte become very close, and he says that if she ever sees anything suspicious, she must tell him.
One day she is with one of the sailors, when his needle snaps. Charlotte offers to get a new one for him from the forecastle, where the crew sleeps. While looking for the needle, she sees a pistol in the trunk, and a round robin on the table. After contemplating whether or not to tell the captain, Charlotte's fear drives her to inform him. Captain Jaggery heads off the rebellion, shooting the stowaway Mr. Cranick, who held a grudge against the captain for lashing his arm so much it had to be amputated. Charlotte is distressed as Captain Jaggery orders Zachariah, one sailor that Charlotte has very strong feelings for, whipped 50 lashes. Charlotte tries to protect Zachariah by grabbing the whip, but accidentally hits the captain's face. Jaggery is enraged and whips Zachariah mercilessly, leading to his death and funeral.
After the captain has withdrawn his protection of Charlotte, she feels compelled to replace Zachariah's place as a crew member, as she feels guilt for her naive part in revealing the crew's plans. The crew allows her to join them after she successfully climbs up and down the tallest mast, the royal yard, on the ship. To climb the ship, she must either use the ratlines or shimmy up the mainmast itself. She chooses the ratlines. While climbing down, she almost falls to her death, but she gets herself untangled. When she comes down, however, the captain is there, and Charlotte tells him she is joining the crew. Annoyed by her change of heart, he dubs her "Mister Doyle" and moves her things from her cabin to the forecastle. Captain Jaggery strikes Charlotte across the face, and she vows to reveal his cruelty to the courts after they complete their voyage and insists that her reasons are justified.
As the Seahawk enters a powerful hurricane, Charlotte falls from the ratlines and is saved by a man whom she believes is Zachariah, despite his apparent death. As she climbs back down, the crew finds the body of the first mate, Mr. Hollybrass, stabbed in the back, by the dirk Zachariah gave her. She is ordered to the brig, where she finds Zachariah, who has been hiding there since he was thrashed nearly to death. Captain Jaggery holds a trial and conveniently finds her guilty of Mr. Hollybrass' murder after accusing Charlotte of being unnatural in many aspects of her life, and comparing this to the unnatural murder of Hollybrass. Captain Jaggery tells Charlotte that he won't be the jury; instead the crew will be the jury. As Charlotte has vowed to expose his cruelty when they land, he threatens to hang her unless she will align herself with him and become a respectable young woman again.
She finds out that Zachariah is actually alive and has been living in the jail of the "Seahawk" with the help of another sailor, Keetch, who supplies him with food. With Zachariah's help, she escapes the prison and plans to usurp the captain's title. Instead, she finds the captain waiting for her. The Captain says that he has been waiting for her all along. Keetch had told him everything. Jaggery reveals that he himself had killed Hollybrass, but claims that he had been threatened and had no choice but to murder him. Not wanting to lose his title, he blames the death on Charlotte. He tells her she has three choices. She can 1) take the muskets and disrespect her family and herself by killing Captain Jaggery, 2) put on her proper clothing and wait at the docks like a proper lady, forgetting all about the fights, and begging him for mercy in front of the crew, or 3) consent to be hanged. She refuses to take any of the choices, and flees the cabin. Jaggery attempts to kill her in front of the crew, but falls off the ship's bowsprit to his death while chasing Charlotte, despite Charlotte's awkward attempt to save him. Zachariah tells the crew that a new captain must be named, and that it should be Charlotte, because she has done what they could not. She is elected by the crew, but serves primarily as a figurehead due to her lack of experience. Zachariah openly exercises the powers of the captain, after she insists on it. They land in Providence, Rhode Island, 12 hours later.
When the Seahawk arrives in Rhode Island, Charlotte returns to her old "proper" behavior and dress. She intends to hide what happened from her family, but her father reads her journal of the voyage. He is appalled by what he sees as "lies" and defamation of Captain Jaggery. He burns the diary and tells Charlotte that she will be punished and reformed. Charlotte finally decides to escape from her home one night, and returns to the Seahawk to be a sailor with Zachariah and the crew.