The story follows Mary Lennox, a sour, unloved orphan sent from India to live in a gloomy Yorkshire manor belonging to her distant uncle, Archibald Craven. Surrounded by hundreds of locked rooms and a vast, desolate moor, Mary feels entirely isolated until she discovers a walled garden that has been locked away for a decade. With the help of a friendly robin and a local boy named Dickon who understands animals and nature, Mary begins to clear away the dead wood and weeds to revive the dormant plants. As she works in the fresh moor air, her bitter disposition melts away, and her frail body grows strong and healthy.
Soon, Mary discovers an even greater secret within the manor: her cousin Colin, a bedridden and spoiled boy who has been convinced by doctors and servants that he is dying of a deformed spine. Mary and Dickon introduce Colin to the secret garden, pulling him away from his dark room and his paralyzing fears. Surrounded by blooming flowers and the vibrant life of the moor, Colin experiences a miraculous physical and emotional awakening.
Standing on his own two legs for the first time, he realizes that his weakness was largely an illusion born of isolation and despair. The novel reaches its emotional peak when Mr. Craven, drawn back to his home by a mysterious premonition, finds his son running and playing in the flourishing garden, completely restored to health and joy.