Coraline Jones and her parents, Mel and Charlie, move into an old mansion that has been divided up into flats and is now known as the Pink Palace Apartments. Due to her parents struggling to complete their gardening catalog, Coraline is often ignored. Coraline meets the landlady's talkative grandson, Wyborne "Wybie" Lovat and a stray black cat who follows him around. Wybie later leaves Coraline a button-eyed rag doll he discovered in his grandmother's trunk that eerily resembles her. Soon after, Coraline discovers a small door in the living room that is bricked up and can only be unlocked with a key that has a button-shaped motif.
During the night, Coraline is awakened by a mouse, who guides her through the door, now a portal to a seemingly more lively version of the house. Coraline meets her Other Mother and Father, button-eyed doppelgängers of her parents that appear more attentive and caring than her actual parents. After having dinner with them, she goes to bed and awakens back in the real world. Wybie tells Coraline about his grandmother's twin sister who disappeared in the house as a child. Coraline's neighbors, Sergei Alexander Bobinsky, an eccentric Chernobyl liquidator-turned gymnast who owns a mouse circus, and retired burlesque actresses April Spink and Miriam Forcible, cryptically warn her about the door and of imminent danger.
Coraline visits the Other World for a second and third time; where each time, accompanied by the mute Other Wybie, she is entertained by the Other Bobinsky's mouse circus and the Other Spink and Forcible. Coraline also encounters the cat, who has the ablities to speak in the Other World and traverse between the two dimensions. The Other Mother soon offers Coraline to stay in the Other World permanently on the condition of having buttons sewn over her eyes. A horrified Coraline rejects the offer and goes to bed, but when she wakes up, she finds she is still in the Other World. When Coraline demands to return home, the Other Mother transforms into a more menacing version of herself and imprisons Coraline in a room behind a mirror. There, Coraline meets the ghosts of the Other Mother's previous child victims, including Wybie's great aunt, who reveal that the Other Mother, whom they call the "Beldam", used the same doll Coraline had, each time designed after the child in question, to spy on them, take advantage of their unhappiness and lure them into her dimension. When they accepted the Beldam's offer of having buttons sewn over their eyes, she trapped their souls. After Coraline promises to free their souls, the Other Wybie helps her escape back to the real world.
Coraline finds her parents missing, eventually realizing that they have been kidnapped by the Beldam. She looks for advice and approaches Spink and Forcible. After being given Spink's lucky adder stone, Coraline soon returns to the Other World accompanied by the cat, where she proposes a game to the Beldam: if she can find the ghost children's souls and her parents, they will all go free, if not, she will finally accept the Beldam's offer. Coraline ventures into the now-hostile Other World using the stone to find the ghost children's souls; hidden as objects belonging to the dimension's inhabitants and with each one she collects, parts of the Other World disintegrate until only the living room remains. Coraline then encounters the Beldam in her true form, a humanoid arachnid with needle-like fingers on her hands. One of the ghost children warn her that even if she succeeds, the Beldam will never let her go. Using this advice, Coraline tricks the Beldam into unlocking the door and, upon finding her parents trapped in a snow globe, creates a diversion by throwing the cat at her. Coraline grabs the snow globe, narrowly escapes through the door with the Beldam in pursuit, and manages to close and lock it with the help of the ghost children, severing the Beldam's right hand in the process.
Coraline's parents reappear in the real world without any memory of what happened to them. That night, the ghost children appear in Coraline's dream to thank her for freeing their souls, but warn her that the Beldam, as long as she is still alive, will never stop looking for the key. Coraline decides to drop it down an old well near her home, but before she does, the Beldam's severed hand attacks her. Wybie arrives and, after a struggle, destroys the hand by dropping a large rock on it. Coraline and Wybie then throw the key and the hand's remnants into the well and seal it shut.
Soon after, Coraline and her parents, who have finally finished their catalog, host a party for their neighbors. Wybie introduces his grandmother and Coraline prepares to tell her story as the cat is last seen walking behind the Pink Palace signpost before disappearing.