It's Kind of a Funny Story tells the story of Craig Gilner, a New York high school student who serves as the novel's narrator. In the early stages of the story, Craig discusses his small circle of friends, his mostly typical childhood, and his problems with stress and depression. These psychological problems escalate after Craig enrolls in Executive Pre-Professional High School. Craig's friends Aaron and Nia also attend this elite academy.
Craig attempts to deal with his problems by seeing psychologists and taking the anti-depressant Zoloft. Yet his efforts are not fully successful; one night, he decides to kill himself by throwing himself off the Brooklyn Bridge. Fortunately, he backtracks on this plan, reaches a suicide hotline, and is advised to check into a hospital and work through his problems. He does so, and enters the world of Six North, an adult psychiatric clinic in Brooklyn.
At Six North, Craig is exposed to individuals with significant problems of their own. He meets Bobby and Johnny, former drug abusers; Humble, a man with aggression issues; Muqtada, who becomes Craig's roommate and mostly refuses to leave his bed; and Noelle, a beautiful girl Craig's own age who cut her face with scissors. Craig and Noelle begin a close friendship that turns into romance by the novel's end. During his stay, Craig discusses his problems with Aaron and Nia and decides to make a change in his life. After leaving Six North, he will transfer out of Executive Pre-Professional and study art.
Before his departure, Craig brings the residents of Six North together in various ways. He screens the movie Blade II, brings in Egyptian music to entertain and enliven Muqtada, and has an intimate encounter with Noelle in his room. At the novel's end, Craig, his parents, and his sister Sarah are walking home from Six North. Craig reflects on the world around him; he has embraced a new, active, joyous approach to life.