Franny and Zooey is composed of two sections, which were originally published in the New Yorker magazine as two separate short stories. The first story or section, Franny, was published in the New Yorker in January 1955. In Franny, Franny Glass meets her boyfriend Lane Coutell for a football weekend at his college. They do not get to join many of the festivities, though, because during their first lunch together, Franny begins to have a breakdown. She tells Lane that she is sick of the phoniness at school and of the egotism of the faculty. She has quit the play she was in because she is embarrassed about what she feels to be acting fake. As she gets worked up, she reveals that she has become interested in the "Jesus prayer," a continuous prayer meant to cleanse one's spirit. Lane mostly brushes off Franny's concerns until she faints on the way to the bathroom. As he is helping to revive her, she begins to speak the prayer.

Zooey basically picks up where Franny left off. First, though, the narrator names himself. The man claiming to be the author of the story is Buddy Glass, one of Franny and Zooey's older brothers. The story resumes. It is the Monday after the weekend Franny's breakdown started, and Zooey is at home in New York City. In his conversation with his mother, Bessie Glass, it is revealed that Franny is now at home, sleeping and crying on the living room sofa. Bessie wants Zooey to talk to Franny, which he eventually does. The two of them have a long theological and personal discussion. We learn that the two of them have basically been raised on a blend of different religions, taught to them by their older brothers Buddy and Seymour. Over the course of this long discussion, Zooey helps Franny sort out her spiritual and personal beliefs, allowing her, by the end, to find peace.