This novel alternates chapters between following Kafka and Nakata. This summary will alternate, but not on a chapter by chapter basis.

Kafka, fifteen, runs away from home to escape his father. His mother and sister left him years before, and he hardly remembers them. He steals money from his father before he leaves. He travels by bus, meeting a young woman named Sakura. She gives him her phone number in case he needs anything while he stays in Takamatsu (where she is going).

Kafka arrives at a hotel, where he claims to be doing a research project. His days consist of exercising, and going to the Komura library where he spends all day reading. There is a young librarian named Oshima there who he becomes friends with. One night, he wakes up outside with blood covering his shirt. He is not hurt. He calls Sakura, and she meets him and brings him to her apartment. They talk and then she lets him sleep in her bed and pleasures him with her hand to help him relax. In the morning he leaves her a note, not wanting to burden her further and goes to Kamura library.

Meanwhile, we read official military records from WWII telling a story of a group of children went to pick mushrooms, and suddenly all passed out. They woke up several hours later, except for one boy named Nakata who did not wake up for a very long time. When he finally did, he had no memory, and could no longer read. Now an adult in his sixties, Nakata can speak to cat and so uses this ability to help people find their lost cats. He is currently looking for one when a cat tells him there is a man who goes to a field and catches cats.

Nakata goes to the field to wait for the man and, after several days, a dog approaches and tells Nakata to follow him. Nakata does, and there he meets a man dressed like Johnnie Walker. He claims to be using cat souls to make a flute that he will use to make a more powerful flute. Nakata, seeing him about to murder a cat he knows, seemingly becomes possessed and kills Johnny Walker. He wakes up sometime later but there is no blood on him. He turns himself in, but the cop ignores him. He predicts it will rain mackerel from the sky the next day, and it does.

By now he has left Tokyo, following the same path as Kafka. He gets the help of a truck driver, who takes him all the way to Shikoku where Kafka is.

Kafka spends several days at the Kamura library, where he befriends the librarian Oshima. Oshima helps him as he discovers he is a runaway and when the cops begin to look for Kafka (because his father has been murdered) he takes him to a family cabin in the mountains where Kafka stays for several days. When he returns, Kafka starts to live in a room in the library where Miss Saeki's (who runs the library) childhood lover lived growing up. He died when they were in their twenties.

Kafka works at the library by day. At night he begins to have visions of a young (15) Miss Saeki visiting the room at night. We learn that Kafka's father told him that he would kill his father and sleep with both his mother and his sister. Kafka falls in love with the young Miss Saeki.

Meanwhile Nakata and his truck driver friend (Hoshino) search for something called the Entrance Stone. With the help of a metaphysical being disguised as Colonel Sanders, Hoshino finds the stone and takes it to Nakata. Hoshino then "opens" the entrance by flipping the stone.

Kafka tells Miss Saeki he thinks she might be his mother. He then asks if she will sleep with him. That night she comes to his room and they sleep together for the first time. She will come for several nights after this.

Sensing the change Oshimo takes Kafka back to the cabin so Miss Saeki can deal with the emotional burden (she was frozen emotionally at the point when her lover died) that is overwhelming her. While at the cabin he has a dream that he violates Sakura and the next day he goes into the woods, where he finds two soldiers who were lost during WWII training. They lead him to a strange town where time doesn't mean anything. While there he meets both 15 year old Miss Saeki, and adult Miss Saeki. The adult version says Kafka "already knows" the answer to whether she is his mother or not. Kafka leaves the village before the entrance is closed otherwise he will be stuck there forever.

Nakata and Hoshino go to the Kamura library. Nakata meets with Miss Saeki, and she asks him to burn her memoirs before anyone can read it. He agrees. When he leaves she dies of a heart attack. Nakata burns the papers, and then they return to their apartment. Nakata dies in his sleep and Hoshino must take care of the stone on his own. While waiting for the right time to close the entrance, a monster emerges from Nakata's body. Hoshino (who was warned by a cat that he must kill it) can't injure it. He kills it by closing the entrance stone.

Kafka returns to the library with Oshimo's brother who implies he once went to the village with the 2 soldiers. Kafka decides to return to Tokyo, hoping to see Sakura again when she goes back to Tokyo. He calls her his sister at the end of the phone call. Oshimo tells him he is always welcome at the library and Kafka says he will return.