The novel centres on Mary Lennox, who is living in India with her wealthy British family.
She is a selfish and disagreeable 10-year-old girl who has been spoiled by her servants and neglected by her unloving parents. When a cholera epidemic kills her parents and the servants, Mary is orphaned. She is sent to England to live with a widowed uncle, Archibald Craven, at his huge Yorkshire estate, Misselthwaite Manor. Mary is brought to the estate by the head housekeeper, the fastidious Mrs. Medlock, who shuts her into a room and tells her not to explore the house. When Martha mentions the late Mrs. Craven’s walled garden, which was locked 10 years earlier by the uncle upon his wife’s death, Mary is determined to find it.
One day, Mary discovers an old key that she thinks may open the locked garden. Shortly thereafter, she spots the door in the garden wall, and she lets herself into the secret garden. She finds that it is overgrown with dormant rose bushes and vines, but she spots some green shoots, and she begins clearing and weeding in that area. One day she encounters Dickon, and he begins helping her in the secret garden. Mary later uncovers the source of the strange sounds she has been hearing in the mansion: they are the cries of her supposedly sick and crippled 10-year-old cousin, her uncle’s son Colin, who has been confined to the house and tended to by servants. He and Mary become friends, and she discovers that Colin does not have a spinal deformation.
Dickon and Mary take Colin to see the garden, and there he discovers that he is able to stand. The three children explore the garden together and plant seeds to revitalize it, and through their friendship and interactions with nature they grow healthier and happier. When her uncle returns and sees the amazing transformation that has occurred to his son and his formerly abandoned garden now in bloom, he embraces his family, as well as their rejuvenated outlook on life.