In 1947, Mary Lennox is found abandoned in her home in British India, her parents having died from cholera and her having been forgotten in the turmoil of Partition. Mary is sent to her uncle, Lord Archibald Craven's Misselthwaite Manor in Yorkshire, England. She is an unpleasant, unkind young girl who has had to repress her own emotions whilst growing up in the Raj.
Upon arriving, she meets Mrs Medlock, a strict and firm lady who is Lord Craven's housekeeper and servant. Mary is instructed to not explore the house and is confined to her room at night. There, she meets Martha, a servant who is unsettled by her demands.
Mary is allowed to leave the house to explore the estate and woods nearby and stumbles upon a stray dog whom she names Jemima. Later that night, she hears tiny screams and wailings throughout the corridors only to find Lord Craven's bedridden son, Colin Craven.
The next day, Mary meets Lord Craven in his study and he tells her to not cause any trouble. Mary continues exploring and follows Jemima into the mist. When she catches up with Jemima, she finds the dog with its leg caught in a trap. She helps Jemima, freeing her from the trap but the dog runs away. Mary follows and climbs a wall and falls into the secret garden.
Mary is then guided by a Robin to a stone statue within the garden which has a key to the garden within it. She leaves the garden as Mrs Medlock calls out for her. Back at the estate, Mary meets with Colin again as he talks about having a hunchback and not being able to walk. She tells him about the garden on the estate but Colin is uninterested. Snooping around later, she finds a room with pictures of both Mary's mother and Grace Craven, and she grabs a souvenir, a pearl necklace.
The next day, Mary returns to the garden to find Dickon, who offers to help heal Jemima. Mary then brings Colin in his wheelchair for the first time to the same room with his mother's pictures and dresses. Both Mary and Dickon hatch a plan to bring Colin to the garden, hoping to heal his immobility, but upon returning, Mrs Medlock confronts Mary for stealing the pearl necklace and she is punished by being signed up for a boarding school. Later, confined and locked in her room, Mary finds letters between her mother and aunt in a rocking horse. She persuades Colin to read them and the three continue reading letters in the garden.
A depressed and distracted Lord Craven, while lighting a candle, sets the desk on fire. The next morning, Mary, Dickon and Colin are in the garden when they see black smoke coming from the house. Colin persuades Mary and Dickon to run to check it out. Mary enters the burning house to find Lord Craven frantically looking for his son in the fire. She tries in vain to convince him to escape as his son is safe outside, but he resists until the ghost of his wife guides them out safely as the fire brigade arrives. An anxious Lord Craven and Mrs Medlock go with Mary and Dickon to Colin in the secret garden. Lord Craven gazes in awe at his son's mobility as they rekindle their relationship.
The film ends with Lord Craven rebuilding the estate and Mary, Dickon and Colin having fun in the secret garden.
