Holden Caulfield, a teenager, is living in an unspecified institution in Southern California near Hollywood in 1951. Caulfield intends to live with his brother D.B, an author and World War II veteran whom Holden resents for becoming a screenwriter, after his release in one month. As he waits, Holden recalls the events of the previous Christmas.
Holden begins his story at Pencey Preparatory Academy, an exclusive boarding school in Agerstown, Pennsylvania, on the Saturday afternoon of the traditional football game with a rival school. Holden has been expelled from Pencey due to poor work and is not to return after Christmas break, which begins the following Wednesday. He plans to return home on that day so that he will not be present when his parents receive notice of his expulsion. After forfeiting a fencing match in New York by forgetting the equipment aboard the subway, he is invited to the home of his history teacher, Mr. Spencer. Spencer is a well-meaning but long-winded old man. Spencer greets him and offers him advice, but embarrasses Holden by further criticizing Holden's work in his subject in a rude manner.
Holden returns to his dorm wearing the new red hunting cap he bought in New York. His dorm neighbor Robert Ackley is one of the few students also missing the game. Ackley, unpopular among his peers, disturbs Holden with his impolite questioning and mannerisms. Holden, who feels sorry for Ackley, tolerates his presence. Later, Holden agrees to write an English composition for his roommate, Ward Stradlater, who is leaving for a date. However, Holden is distressed to learn that Stradlater's date is an old friend, Jane Gallagher, whom Holden had romantic feelings for and feels protective of. That night, Holden decides to go to a Cary Grant comedy with his best friend Mal Brossard and Ackley. Since Ackley and Mal had already seen the film, they end up just playing pinball and returning to Pencey. When Stradlater returns hours later, he fails to appreciate the deeply personal composition Holden wrote for him about the baseball glove of Holden's late brother Allie, and refuses to reveal whether he slept with Jane. Enraged, Holden punches him, and Stradlater easily wins the ensuing fight. When Holden continues insulting him after the fight, Stradlater knocks him unconscious and leaves him with a bloody nose. After leaving for Ackley's room, Holden is disappointed when he treats him rudely. Fed up with the so-called "phonies" at Pencey Prep, Holden impulsively decides to leave Pencey early, sells his typewriter to earn money, and catches a train to Penn Station in New York. Holden intends to stay away from his home in a hotel until Wednesday, when his parents would have received news of his expulsion. Aboard the train, Holden meets the mother of a wealthy, obnoxious Pencey student named Ernest Morrow, and lies to her about himself and her son.
In a taxicab, Holden inquires with the driver about whether the ducks in the Central Park lagoon migrate during winter, a subject he brings up often, but the man barely responds. Holden checks into the dilapidated Edmont Hotel. He spends an evening dancing with three tourist women from Seattle in the hotel lounge and enjoys dancing with one, though is disappointed that he is unable to hold a conversation with them. Following an unpromising visit to Ernie's Nightclub in Greenwich Village, Holden becomes preoccupied with his internal angst and agrees to have a prostitute named Sunny visit his room. His attitude toward the girl changes the minute she enters the room; she seems about the same age as him. Holden becomes uncomfortable with the situation, and when he tells her all he wants to do is talk, she becomes annoyed and leaves. Even though he still paid her the right amount for her time, she returns with her pimp Maurice and demands more money. Holden insults Maurice, and after Sunny takes the money from Holden's wallet, Maurice punches him in the stomach and leaves with Sunny. Afterwards, Holden imagines that he has been shot by Maurice, and pictures murdering him with an automatic weapon.
The next morning, Holden, becoming increasingly depressed and in need of personal connection, calls Sally Hayes, a familiar date. Although Holden claims that she is "the queen of all phonies", they agree to meet that afternoon to attend a play at the Biltmore Theater. Holden shops for a special record, "Little Shirley Beans", for his 10-year-old sister Phoebe. He spots a small boy singing "If a body catch a body coming through the rye", which lifts his mood. Although Holden's date initially goes well, it soon sours after Sally introduces her friend George. After the play, Holden and Sally go ice skating at Rockefeller Center, where Holden suddenly begins ranting against society and frightens Sally. He impulsively invites Sally to run away with him that night to live in the wilderness of New England, but she is uninterested in his hastily conceived plan and declines. The conversation turns sour, and the two angrily part ways.
Holden decides to meet his old classmate, a Columbia student named Carl Luce, for drinks at the Wicker Bar in the Seton Hotel. During the meeting, Holden annoys Carl with his fixation on sex. After Luce leaves, Holden gets drunk, awkwardly flirts with several adults, and calls an icy Sally. Exhausted and out of money, Holden wanders over to Central Park to investigate the ducks, breaking Phoebe's record on the way. Nostalgically recalling his experience in elementary school and the unchanging dioramas in the Museum of Natural History that he enjoyed visiting as a child, Holden heads home to see Phoebe. He sneaks into his parents' apartment while they are out, and wakes up Phoebe – the only person with whom he seems to be able to communicate his true feelings. Although Phoebe is happy to see Holden, she quickly deduces that he has been expelled, and chastises him for his aimlessness and his apparent dislikes towards everything. When asked if he cares about anything, Holden shares a selfless fantasy he has been thinking about (based on a mishearing of Robert Burns's Comin' Through the Rye): he pictures himself as the sole guardian of thousands of children playing in a huge rye field on the edge of a cliff. His job is to catch the children if, in their abandon, they come close to falling off the brink; to be, in effect, the "catcher in the rye". Because of this misinterpretation, Holden believes that to be the "catcher in the rye" means to save children from losing their innocence.
When his mother returns home, Holden slips out and visits his former and much-admired English teacher, Mr. Antolini, who is now a New York University professor. Mr. Antolini expresses concern that Holden is headed for "a terrible fall" and advises him to begin applying himself. Although Holden is exhausted, he is courteous and considers his advice. Mr. Antolini also provides Holden a place to sleep. Holden is upset when he wakes up in the night to find Mr. Antolini patting his head, which he interprets as a homosexual advance. Confused and uncertain, he leaves and spends the rest of the night in a waiting room at Grand Central Station, where he sinks further into despair and expresses regret over leaving Mr. Antolini. He spends most of Monday morning wandering Fifth Avenue.
Losing hope of finding belonging or companionship in the city, Holden impulsively decides that he will head out west and live a reclusive lifestyle as a gas station attendant. He decides to see Phoebe at lunchtime to explain his plan and say farewell. While visiting Phoebe's school to give a forged excuse note, Holden becomes obsessed with graffiti containing the word "fuck", and becomes distressed by the thought of children learning the word's meaning. When he meets Phoebe at the Metropolitan Museum of Art, she arrives with a suitcase and asks to go with him, even though she was looking forward to acting as Benedict Arnold in a play that Friday. Holden refuses to let her come with him, which upsets Phoebe, so Holden decides not to leave after all. He tries to cheer her up by allowing her to skip school and taking her to the Central Park Zoo, but she remains angry with him. They eventually reach the zoo's carousel, where Phoebe reconciles with Holden after he buys her a ticket. Holden is finally filled with happiness and joy at the sight of Phoebe riding in the rain.
In a short epilogue, Holden briefly alludes to encountering his parents that night and "getting sick" (implying a tuberculosis diagnosis), mentioning that he will be attending another school in September. Holden says that he doesn't want to tell anything more because, surprisingly, he has found himself missing his former classmates. He warns the reader that telling others about their own experiences will lead them to miss the people who shared them.