At the turn of the 20th century, Mary Lennox is a sickly and unloved 10-year-old girl, born in India to wealthy British parents who never wanted her. She is cared for by servants, who allow her to become a spoiled, aggressive and selfish child.
After a cholera epidemic kills her parents and the servants, Mary is discovered alive but alone in the empty house. She briefly lives with an English clergyman and his family before she is sent to Yorkshire, England to live with Archibald Craven, an uncle whom she has never met, at his isolated house, Misselthwaite Manor.
At first, Mary is as rude and sour as ever. She dislikes her new home, the people living in it, and most of all, the bleak moor on which it sits. However, a good-natured maid named Martha Sowerby tells Mary about the late Mrs Craven, who would spend hours in a private walled garden growing roses. Mrs Craven died after an accident in the garden, and the devastated Mr Craven locked the garden and buried the key. Mary becomes interested in finding the secret garden herself, and her ill manners begin to soften as a result. Soon she comes to enjoy the company of Martha, the gardener Ben Weatherstaff, and a friendly robin redbreast. Her health and attitude improve, and she grows stronger as she explores the moor and plays with a skipping rope that Mrs Sowerby buys for her. Mary wonders about both the secret garden and the mysterious cries that echo through the house at night.
As Mary explores the gardens, her robin draws her attention to an area of disturbed soil. Here Mary finds the key to the locked garden and eventually the door to the garden itself. She asks Martha for garden tools, which Martha sends with Dickon, her 12-year-old brother. Mary and Dickon take a liking to each other, as Dickon has a kind way with animals and a good nature. Eager to absorb his gardening knowledge, Mary tells him about the secret garden.
One night, Mary hears the cries once more and decides to follow them through the house. She finds a boy named Colin living in a hidden bedroom. She soon discovers that they are cousins, Colin being the son of Mr and Mrs Craven, and that he suffers from an unspecified spinal problem. Mary visits him every day that week, distracting him from his troubles with stories of the moor, Dickon and his animals, and the secret garden. Mary finally confides that she has access to the secret garden, and Colin asks to see it. Colin is put into his wheelchair and brought outside into the secret garden. It is the first time he has been outdoors for years.
While in the garden, the children are surprised to see Ben Weatherstaff looking over the wall on a ladder. Startled and angry to find the children in the secret garden, he admits that he believed Colin to be a cripple. Colin stands up from his chair and finds that his legs are fine, though weak from long disuse. Colin soon spends every day in the garden, sometimes with Dickon as company. The children conspire to keep Colin's recovering health a secret, so as to surprise his father, who is travelling abroad. As Colin's health improves, his father sees a coinciding increase in spirits, culminating in a dream where his late wife calls to him from inside the garden. When he receives a letter from Mrs Sowerby, he takes the opportunity finally to return home. He walks the outer garden wall in his wife's memory, but hears voices inside, finds the door unlocked, and is shocked to see the garden in full bloom, and his son healthy. The servants watch, stunned, as Mr Craven and Colin walk back to the manor together.
