Mary Lennox (Kate Maberly
) is a ten year old British girl living in India around the cusp of the 20th century. Her parents (Irène Jacob
and Colin Bruce
) are neglectful, leaving her in the care of an Aya (Parsan Singh
), a native servant, while they attend parties and partake in other leisures and obligations. This leaves Mary with a sour disposition and all the anger and bitterness of someone twice her age. Her anger leads her to act out, but she never cries. One night, while her parents are away at a nearby party, Mary breaks her mother's small, ivory elephant and hides with the pieces under her parent's bed. Suddenly, the earth shakes and things in the room begin to fall off their counters and break. Elephants roar and people outside scream as the earthquake continues. Mary's parents both perish in the devastation and she is left alone.
Six months after the incident, Mary arrives by ship in Liverpool, England where she is picked up by Mrs. Medlock (Maggie Smith
), the head keeper of Misselthwaite Manor in Yorkshire. The manor is owned by Mary's sullen uncle, Lord Archibald Craven (John Lynch
) whose late wife was the twin sister of Mary's mother. Mrs. Medlock instructs Mary to keep out of trouble and not to disturb her uncle, who would rather not see her at all, while she finds ways to amuse herself. Mary is dissentful towards the manor which appears cold and dank among the wintry grounds it sits on. However, she finds a kind heart in her servant, Martha (Laura Crossley
), the daughter of one of the cooks. Martha is patient with the angry Mary, and assists with her dressing and amusement, giving her a jump rope as a gift. She also speaks of her brother Dickon (Andrew Knott
) who is around Mary's age and may provide her additional company while Martha works.
Mary soon discovers that the manor holds many secrets and mysteries. She hears crying at night and, when she questions the servants, they deny the sounds. One evening she finds a hidden door in her room that leads to abandoned sectors of the manor. She discovers one particular room, dusty but brightly decorated, that she is interested to find belonged to her aunt. An ivory elephant, one identical to her mother's, sits on the bureau inside of which Mary finds a key. During one of her daily explorations of the grounds, Mary meets an old gardener named Ben Weatherstaff (Walter Sparrow
) who warns Mary not to go snooping about, though he tells her that she reminds him of the late mistress. When Mary inquires about the grounds hidden behind a large stone wall, Ben tells her that it was a garden owned by Mrs. Crane and that it's since been locked away to anyone since she died. When he leaves, Mary is met by a red-breasted robin which leads her to the ivy covered wall and a secret doorway hidden within. Through the keyhole, Mary can see the expanses of a large garden. Remembering the key she found, Mary fetches it and tries it on the door: it fits. Inside, she finds that the garden is overgrown and appears dead in the chill air.
Having originally thought that her uncle wanted nothing to do with her, Mary is surprised when she is summoned to meet him. She is brought to his study where she sees her crook-backed uncle for the first time. He is saddened to see that Mary looks just like her mother and, therefore, like his wife. Though he contemplates sending her to better accomodations at a boarding school, Mary begs to stay at the manor, asking only for a bit of earth to grow things in. Craven allows her to stay and bids her leave before he packs and leaves the manor, fleeing the coming spring, Mary theorizes. The staff at the manor speak of her uncle as a cursed man, forever enveloped in grief since the loss of his wife.
Mary goes to visit her garden again and comes across the nature-loving Dickon. She shows him the garden on oath of secrecy and he relieves her worries of its health when he shows her that all the plants in the garden are still alive, just asleep. He helps her remove invasive weeds and shows her the proper way to plant flower bulbs. Mary smiles again. When she notices a swing hanging from a nearby tree, Dickon tells her that Mrs. Craven died falling from it.
One night, Mary dreams of her mother. As her toddler self begins to cry after losing her mother, Mary awakens to the sound of real crying. She takes a candle and follows the sounds to a chamber she's never seen. Inside, a boy her age lies in a large bed and, when he sees her, stops his crying and beckons her forward. He introduces himself as Colin Craven (Heydon Prowse
), the master of the house while his father's away. The children learn they are cousins and Colin tells Mary how he's never left the house and cannot walk while displaying his morbid obsession with death. He tells her that his mother died giving birth to him and, being so weak, was fed the notion that he will remain so until he develops a hunch like his father and then die. Medlock tends to Colin personally and rigorously instructs the other servants to provide for him. Mary, however, cannot see anything wrong with Colin besides the fact that he's cooped up inside all the time. His selfish behavior angers her further, though she regularly visits him while being sure to avoid Medlock who would highly disapprove.
One day Mary, sickened by Colin's despondence and convinced that all he needs is some light, opens the closed windows and puts Colin in his wheelchair to sit by them. She leaves him in his room, but the light blinds him and, when he sees Mary outside with Dickon, he begins to throw a tantrum and falls out of his chair. The concerned servants place Colin on the bed where he continues to scream until Mary returns and begins massaging his back. When Medlock finds them together, she demands that Mary leave until Colin orders her to let them be. With Mary's encouragement, Colin finally decides that he may be ready to venture outside and makes the announcement to all the servants that he, Mary, and Dickon, will explore the grounds alone. Mary and Dickon take Colin in his wheelchair to the garden his mother used to tend. He is in awe and is convince that the place is filled with hidden magic. When old Ben discovers them, he blurts out that Colin is naught but a cripple. Offended, Colin stands for the very first time.
As spring arrives and flowers bloom and animals are born, the children continue to visit the garden together and Colin grows stronger by the day, eventually learning to walk. They decide to keep his progress a secret and wish to surprise Lord Craven when he returns. Medlock, however, sees Mary as a threat to Colin's health and is convinced that her wild ways and disobedience will prove fatal to the boy.
The children visit the garden every day and Mary and Dickon grow close. Colin expresses his love for Mary but she assures him that they will always be together as they look at photographs of their mothers. Colin feigns weakness in front of Medlock and the servants though he is against his old treatments, including taking ice baths to soothe his 'swollen' legs. Medlock soon grows convinced that Colin and Mary should be separated and she locks them in their rooms, intent on keeping them there until Craven's return. However, Mary escapes through the secret door in her room and reunites with Colin and Dickon. They escape the manor and run to the garden in the middle of the night to perform a magic rite to summon Colin's father home and set his spirit free.
Craven, meanwhile, dreams of his wife and hears her calling him to her garden. He wakes with a start and immediately heads home. The servants are surprised to see him home unannounced and scramble to accompany him, including Medlock. He demands to see his son but, when they walk into an empty room, Medlock tells him that it must be because of Mary. They go to her room to find it also empty and Craven resolves to follow his wife's words. He leaves the distraught Medlock in the manor as he walks towards the garden where he hears laughter and finds the secret door open. He walks inside where he finds Colin blindfolded, but walking, playing blind man's bluff. Mary and Dickon emerge from their hiding spots as Craven approaches Colin. Thinking the figure is Dickon, Colin reaches up to touch his father's face before removing his blindfold in surprise. Father and son embrace one another in happiness but Mary runs away, saddened and thinking that no one wants her.
Dickon tries to console her, but she runs off alone. Colin and Craven soon find her and Craven tells her that every miracle that has happened (the garden growing once more, Colin's strength, and now Craven's return to the place he thought he'd never see again) is because of her and she IS wanted. Everyone returns to the manor where the servants and Medlock are astounded to see Colin walking and running beside his father. Dickon rides his white pony over the Yorkshire estate as Mary narrates that her uncle learned to laugh, she learned to cry, and the garden remained open to all. And, if you look the right way, you can see that the whole world is a garden.