The Perks of Being a Wallflower was first published on February 1, 1999 by Pocket Books through its MTV Books imprint. It became the subsidiary's best-selling book with 100,000 copies in print as of 2000, and was included on school reading lists and gathered a cult following. In spite of it, The Perks of Being a Wallflower has appeared six times on the American Library Association's list of 10 most-frequently-challenged books. Usually, there are request to remove it from high school public libraries because it deals with drugs use among teenagers, homosexuality, suicide, and has sexually explicit scenes and "offensive language." Since Chbosky "didn't write it to be a controversial book," he was surprised by the bans.
Critical response was mixed; Publishers Weekly called the novel "trite", dealing with "standard teenage issues" in which "Chbosky infuses a droning insistence on Charlie's supersensitive disposition." Although Kirkus Review said it had "the right combination of realism and uplift", the reviewer criticized Chbosky's "rip-off" of J. D. Salinger's The Catcher in the Rye. Although other reviewers made similar comparisons, Chbosky said he "was not trying to mimic [Salinger's] style as a writer"; he saw "how readers could compare Charlie to Salinger's Holden Caulfield", but "they are very different people with unique problems and perspectives".
Francisca Goldsmith of the School Library Journal said the novel "cleverly" makes the readers the recipients of Charlie's letters, and it "will engage teen readers for years to come." Common Sense Media's Kate Pavao praised its relevant themes for teenagers: "Readers will find themselves quickly feeling sorry for the protagonist and worrying about him throughout his transformative journey." In an Amazon.com review, Brangien Davies wrote: "What is most notable about this funny, touching, memorable first novel from Stephen Chbosky is the resounding accuracy with which the author captures the voice of a boy teetering on the brink of adulthood." For The A.V. Club, Marah Eakin wrote that although for an adult "Perks suffers from an overabundance of pure, raw angst ... unlike some more arrested development-friendly YA fare like Harry Potter, Perks speaks to a more specific age range and does it well."
With the announcement of a film adaptation the novel received more attention; it sales increased from 88,847 copies in 2011 to 425,933 in 2012, and it reached the New York Times bestseller lists. It entered the Children's Paperpack Books category on the June 23, 2012 list, and had 1.5 million copies in print in November 2012. As of May 11, 2014 it appeared on The New York Times top 10 list for the 71st non-consecutive week, and was in the top 15 on the November 23 list. The novel has been published in 16 countries in 13 languages.