The book, Chbosky's first novel, was published by MTV Books in 1999, and was an immediate popular success with teenage readers; by 2000, the novel was MTV Books' best-selling title, and The New York Times noted in 2007 that it had sold more than 700,000 copies and "is passed from adolescent to adolescent like a hot potato." Wallflower also stirred up controversy due to Chbosky's portrayal of teen sexuality and drug use. The book has been banned in several schools and appeared on the American Library Association's 2006 and 2008 lists of the 10 most frequently challenged books.
In 2000, Chbosky edited Pieces, an anthology of short stories. The same year, he worked with director Jon Sherman on a film adaptation of Michael Chabon's novel The Mysteries of Pittsburgh, though the project fell apart by August 2000. Chbosky wrote the screenplay for the 2005 film adaptation of the Broadway rock musical Rent, which received mixed reviews. In late 2005, Chbosky said that he was writing a film adaptation of The Perks of Being a Wallflower.