The idea of anonymous letters came from a real experience; during his senior year in high school, Chbosky wrote an anonymous letter to Stewart Stern about how Rebel Without a Cause had influenced him. A year and a half later, Stern found Chbosky and became his mentor. By using a series of letters from Charlie to an anonymous character, Chbosky found "the most intimate way" to talk directly to the reader. He thought the letters would help him keep the story cohesive, "to convey the highs and lows of being young—one day, you're on top of the world and you’ve had the greatest of times".
Critics have identified primary themes of teenage reality and (for adults) nostalgia. According to David Edelstein of the New York Magazine, Chbosky captures the "feeling [that] you belong when among friends, yet you'd soon be alone" and notes that "the pain of loss ... [is] almost as intense as the bliss ... it's nostalgia with an emphasis on nostos, pain [sic]." Word Riot 's Marty Beckerman said that The Perks of Being a Wallflower connects with young people because its scenes are "so universal and happen to so many teenagers." Chbosky wanted to convey respect for teenagers, to "validate and respect and celebrate what [teenagers] are going through every day", and said that the novel is for "anyone who's felt like an outcast."
Although it is also read by adults, The Perks of Being a Wallflower is targeted at a teenaged audience. The book addresses a range of themes (including sex and drugs) dispassionately. Other themes include friendship, body image, first love, suicide, eating disorders and sexuality. Chbosky appreciates the importance of entertainment in adolescence: "Books, songs, and movies are more than entertainment when we're young. They help all of us discover who we are, what we believe, and what we hope our life can be." As such, there are several cultural references: musical (The Smiths and Fleetwood Mac), literary (This Side of Paradise, On the Road, To Kill a Mockingbird) and theatrical (The Rocky Horror Picture Show).