Tom is a young boy forced to spend his summer quarantine away from his family in a sterile apartment building. Frustrated by the lack of outdoor space and children his age, he feels powerless against adult decisions. His natural curiosity leads him to investigate a strange grandfather clock, which opens a door to a midnight garden where he finds freedom.

Hatty is an orphaned Victorian girl living with her wealthy relatives in a large manor house. Socially isolated and confined to the estate's grounds by her strict aunt, she creates a fantasy world where she claims to be an imprisoned princess. She is observant enough to spot Tom when others cannot, eventually sharing her secret garden hiding places with him.

Grace is the wealthy matriarch of the Melbourne household who took in her orphaned niece out of obligation rather than love. She constantly belittles Hatty, calling her a charity case while ensuring she remains isolated from society. She enforces rigid expectations on the girl while letting her own sons roam freely.

Mrs. Bartholemew is the cantankerous landlady who owns the converted manor house and lives in the top-floor apartment. She is highly protective of her antique grandfather clock, warning the building's tenants never to touch it. Her demands for quiet make her an intimidating presence to the residents.

Alan is Tom's stern uncle who takes him in during a family illness. He expects strict obedience, insisting that Tom stay in bed for ten hours every night regardless of whether the boy can actually sleep. He approaches life with rigid logic and struggles to relate to his nephew's energetic nature.

Gwen is Tom's aunt, a well-meaning woman who lacks experience with children. She attempts to make her nephew feel welcome by feeding him rich foods and trying to create a cozy environment, though she often misreads what a young boy actually wants.

Peter is Tom's brother who remains at home recovering from a contagious illness. Confined to his bed, he relies on Tom's regular letters to stay entertained and connected to the outside world.

Abel is the Melbourne family's gardener during the Victorian era. He is a deeply religious, weather-beaten man who views anything supernatural with deep suspicion. Despite his rough exterior, he is keenly aware of the household dynamics and acts as a silent protector for the vulnerable.

James is the most thoughtful of the three Melbourne brothers. While he generally participates in his siblings' rough games, he occasionally stops to comfort his cousin when she is distressed.

Edgar is one of Hatty's older cousins. Taking after his mother's harsh disposition, he goes out of his way to tease his younger cousin and actively tries to get her into trouble with the household authorities.

Hubert is the third Melbourne brother, part of the active trio that dominates the Victorian garden. He follows the pack in dismissing his younger female cousin.

Barty is a young man with a gig who enjoys winter sports. He is a polite and friendly presence on the ice, offering assistance to those caught far from home during the river thaw.

Pincher is the Melbourne family dog. Unlike most of the human residents of the manor, the dog possesses a heightened awareness of unusual presences in the garden.