Coraline Jones moves from Pontiac, Michigan with her mother and father to the Pink Palace Apartments in Ashland, Oregon. The other two apartments are lived in by retired actresses Misses Spink and Forcible, and the eccentric Russian acrobat Mr Bobinsky. With her parents desperately working on a gardening catalog in order to make ends meet, and paying only little attention to her, Coraline begins to feel neglected and left out. While exploring the grounds, she meets Wybie Lovat, the chatty grandson of the landlady. Back in the house, Coraline finds an oddly small door that has been wallpapered over. She gets her mother to unlock it, but she finds a brick wall behind it.

That night, Coraline is awakened by the sound of a mouse and follows it to the small door in her living room. She saw that the brick door is gone, suddenly replaced by a long corridor to another door. At the other end, Coraline finds herself in the "Other World," which is the exact same as her house but with different object and other weird things, the house is lived by her   "Other Mother" and "Other Father", decoys of her parents, except for having black buttons eyes. The others pay attention to Coraline. She decides to stay the night in the Other World, but when she wakes up the next morning, she finds herself back in her bed in the real world!

Coraline keeps going to the Other World at night, and is entertained by other versions of her neighbours, including an Other Wybie, who has now sewed up lips by the Other Mother. During her visit, Coraline meets the black cat from her own world. Having the ability to talk in the Other World, it warns Coraline of the dangers of the place, but Coraline doesn’t listen to him. That evening, the Other Mother invites Coraline to stay in the Other World forever. Coraline is ready to accept until she is told she must have buttons sewn on her eyes. She hates the idea and tries to return home. This makes the Other Mother very angry, who transforms into a taller and evil version of her, Coraline is thrown into a small room. There, she meets the ghosts of children who had lost their eyes and souls to the Other Mother. The Other Wybie helps Coraline go back to her home in the real world but Coraline finds her parents have disappeared too. Coraline tries to tell Wybie about the Other Mother and Other World but he can’t talk. That same night the cat shows her that her parents have been kidnapped by the Other Mother in a place hard to find. With no other choice but to return to the Other World, with a seeing stone given to her by Spink and Forcible, Coraline sets out to free the ghost children and rescue her parents.

On the advice of the cat, Coraline challenges the Other Mother to a game. If she can find her parents and the eyes of the ghost children, everyone goes free, if she loses, she will stay in the Other World forever and have the buttons sewn into her eyes. With the help of her seeing stone, the black cat, and the Other Father, Coraline tricks her other mum into opening the door to the real world while she gets the snow globe within which her parents are prisoned in. Coraline escapes; closing the door to the Other World but with the other mother’s hand. Coraline locks the door in the real world and finds her parents safe and sound, with no memory of the experience.

The next night, Coraline thanked by the ghost children one last time. They tell her she is still in danger while she has the door key. To keep the Other Mother from ever kidnapping another child, Coraline drops the key down a well in her garden. The Other Mother's hand, which has made its way into the real world, stalks and attacks Coraline. Wybie discoverers the truth in Coraline's story, he arrives in time to save her and destroy the hand. They throw the hand and the key into the well and seal it very well.

With their catalog complete, Coraline's parents are finally able to spend time with her. They have a garden party for her and the neighbours, including Wybie’s old grandmother - whose long-ago lost sister was one of the ghost children and Coraline, tell her story to her.