In 1946, 38-year-old Lady Mary Craven, Cherie Lunghi, visits an American orphanage and shares news of an exchange program that would allow one child to travel to England and stay at Misselthwaite Manor, now functioning as an orphanage. There, she meets young Lizzie Buscana, Camilla Belle, who is in the garden trying to tend her mother's rose bush. Lady Mary explains the program and the existence of the secret garden, and Lizzie eagerly volunteers to participate so she can see the garden herself.
Lizzie arrives in England and is greeted at the train station by Martha Sowerby, Joan Plowright, who runs Misselthwaite Manor. Lizzie quickly learns that the children are only allowed in the garden on Sundays after church, must behave impeccably, and must not touch anything.
Making friends with Geraldine, Steven and Robert (Aled Roberts), Lizzie explores the garden after curfew and realizes she must help it come back to life. Returning to the manor, Lizzie notices a fire in Robert's room, caused by him falling asleep with a candle still lit. After she raises the alarm and helps extinguish it, Martha questions why Lizzie is still dressed and how she knew there was a fire. Lizzie admits the illicit garden visit, and Martha discovers that Lizzie stole the key to the garden. She learns that Geraldine told Lizzie about the key, but Martha believes the key should belong to Lizzie, suggesting the garden has chosen her over Martha, who could not find the door.
Geraldine, who feels jealous of Lizzie, learns that Ms. Sowerby gave the key to Lizzie and persuades Steven to steal it in revenge for Lizzie's rejection of his affections. When Lizzie realizes the key is missing, she suspects Robert, given his animosity toward her. She sets out to find the key with Robert and discovers that Steven, acting on Geraldine's instructions, took it and threw the key into the pond. Lizzie confronts Geraldine, who initially denies it but finally confesses after Martha disciplines her for lying.
Lizzie is told that she might not need the key after all because of the magic door. As Martha prepares to meet Lady Mary, who has returned to Misselthwaite, Mary notes the garden's revived vitality despite Martha's earlier claims of neglect. Lizzie realizes the garden has thrived on the love and laughter of the children, and with Robert's help she gathers the orphans—Geraldine included—who rush to the quickly revitalized garden.
Lady Mary and Sir Colin Craven, Leigh Lawson, arrive with Martha and are astonished to see the garden thriving rather than dead as Martha had described. Lizzie tells Lady Mary that the garden needs love and should remain open for all the children to enjoy. Lady Mary explains that the garden belongs to her and recalls how it once flourished thanks to a girl from across the sea, and she suggests that it is up to Lizzie to decide its fate. Lizzie proclaims that the garden will stay open so every child can share in its revival.
