Before surgery for his heart, a young boy named Sho is sent to his family's estate to rest by his Aunt. The estate is is comprised of a small house amid a sprawling green landscape.
During his first moments on the grounds, Sho views the house cat, Niya, who is looking at something in some plants. After Niya leaves, Sho catches sight of what appears to be a miniature human.
This is Arrietty, the daughter of a family of 'Borrowers' that live in a dwelling under the house's floorboards.
Arrietty returns to her parents, where her father Pod informs her and her mother Homily about Sho's arrival. Though Homily fears for their safety, Pod reassures the family that Sho has a heart condition, so he probably won't cause them much trouble.
Arrietty is relieved, as her father had intended to take her on her first 'borrowing' within the walls of the house. Later on that evening, she accompanies her father on a quest to obtain a cube of sugar and some tissue paper.
The they get the cube of sugar from the kitchen. For the tissues, Arrietty and Pod climb to the house's second floor, where they make their way through an intricate dollhouse and into a guest bedroom. The two attempt to get the tissue paper, but Arrietty freezes when it seems that Sho has seen her! In her attempts to leave, she drops the sugar cube. As she and Pod leave, Sho addresses her, asking if she is like the little people that his Mother told stories about.
When they return empty-handed, Pod makes up an excuse that his light gave out.
The next day, Arrietty is surprised when the boy stops near a grate near their home and leaves a cube of sugar and a small note. Arrietty tells her parents about this, and Homily is informed by Pod that knowledge of their presence may mean they will have to leave their home.
Arrietty ponders what to do, and returns to the sugar cube. Upon reading the note ("you left something behind"), she takes the items, and climbing up to the second floor, addresses Sho through his window. Returning the cube, she requests that he leave their family alone. However, the moment is interrupted when a crow attempts to eat Arrietty and ends up stuck in the wire mesh of the window. Sho saves Arrietty from falling and hides her as the housekeeper Haru comes in, managing to get the crow loose. After she leaves, Sho realizes that Arrietty has snuck off.
Attempting to return home, she encounters Pod, who informs her and Homily later on that they will have to move.
In the evening, Sho has dinner with his Aunt and Haru. Sho's conversation turns to the dollhouse, and his Aunt explains that their father told her and Sho's Mom that it was made for the little people that he had seen. After dinner, all three go upstairs to appreciate the detailed intricacy of the house.
Later on, as Arrietty and Homily stitch sacks to carry their belongings, Pod comes home with the help of another Borrower named Spiller. Pod has twisted his ankle. The existence of another Borrower fills Arrietty and Homily with hope that they aren't the last of their kind, and Spiller agrees to help them find a new place.
After he leaves, Pod explains to Arrietty that before she was born, there were 2 other families of Borrowers that lived in the house. One of them disappeared, and the other moved away.
Suddenly, the dwelling is shaken as the ceiling is removed. Though it seems that they have been discovered, it is actually Sho, who removes the family's small kitchen, and replaces it with the one in the dollhouse upstairs.
However, the gesture of kindness does nothing more than increase the family's determination to leave. After recovering from his sprain, Pod leaves to search out Spiller and a new place, while Homily continues to pack. Meanwhile, Arrietty finds Sho out in the garden with Niya. Though Sho seems happy to have gifted the kitchen to the Borrowers, Arrietty confesses that his knowledge of their existence has caused her family to prepare to move away.
Sho asks if he can look at her, to which she doesn't say anything, as it makes no difference anymore. He tells her she's beautiful. Then he asks questions about Borrowers and says that there must be very few left and soon there will be none, that's fate. To which Arrietty gets upset and says it's his fault they have to leave, but they're going to survive, they are not going to die. Sho apologizes and says that she's right, he's the one who's going to die. He tells her about his heart condition and hopes she can forgive him for everything. Arrietty is taken aback by this confession and seems deeply affected and saddened to find out about his sickness.
Haru finds the Borrowers' home, with Homily in the dollhouse kitchen, and takes her and puts her in a jar, making sure she can breathe in there. Then she calls a pest control company saying she wants trapping service for something in the house that she doesn't want killed.
When Arrietty finds that her mother was taken she goes to Sho and he helps rescue her. He also takes the dollhouse kitchen back in the dollhouse in his room, so when Haru tries to prove what she saw, she has nothing.
Arrietty's family leaves. They are followed by Niya, the cat, who goes back and brings Sho to say goodbye. He brings a sugar cube as a gift, and Arrietty gives him her hair clip, for good luck with his oncoming heart surgery.
The Borrowers are sailing away in a teapot with Spiller. Arrietty looks sad and Spiller awkwardly offers her a fruit. He's very happy when she takes it. A fish swimming in the shallow water catches her interest, seeming huge next to them. The film ends on a serene, yet kind of sad, note.