Melville initially proposed to his publisher that Pierre be published anonymously and credited "By a Vermonter". He wrote to his British publisher, Richard Bentley that his new book, Pierre
- possessing unquestionable novelty ... [is] as I believe, very much more calculated for popularity than anything you have yet published of mine – being a regular romance, with a mysterious plot to it & stirring passions at work, and withall, representing a new & elevated aspect of American life... 
When it was published in July 1852, it bore the author's real name and was immediately met with negative critical response. One review which ran in the New York Day Book bore the title "Herman Melville Crazy" while the American Whig Review wrote that Melville's "fancy is diseased".
Brian Higgins and Hershel Parker characterize the novel as "an ambitious experiment in psychological fiction" whose primary focus is the "complex workings of the human psyche," especially the "tortuous processes of distortion and self-deception involved in fervid states of mind combining religious exaltation and sexual arousal." They comment that the novel also draws on the conventions of Gothic fiction. Andrew Delbanco added that Pierre long suffered from being in the shadow of Moby-Dick, but that "with its themes of sexual confusion and transgression" it now seems "fresh and urgent."
Delbanco argues that Melville anticipates Sigmund Freud’s assertion that the sexual behavior of each human being transgresses “the standard of normality” to some extent. The novel, Delbanco feels, is ambivalent in dealing with the “rather too loving” supervision of his mother and his “ardent sentiment” for Glen, the young man who is his cousin, with whom he explored “the preliminary love-friendship of boys.” Yet, continues Delbanco, after an extended discussion, it is hard to know whether critics who now see Melville as a homosexual are simply making a long overdue acknowledgment or whether gay readers are projecting their own feelings onto Melville – or both. The novel is, after all, subtitled “The Ambiguities.” Delbanco concludes that “the quest for a private Melville has usually led to a dead end, and we are not likely to fare better by speculating about his tastes in bed or bunk.”
Readers, says Parker, have long been puzzled and critics bothered by the inconsistencies between the character of Pierre in the beginning of the novel and his suddenly becoming an author in later chapters. Parker reasons that the reason for this change is biographical, not artistic. He deduces that Melville took a far shorter manuscript to New York for delivery to Harpers.  The publisher was not at all pleased to see a psychological novel which delivered sexual and literary shocks and threatened to further damage their religious audience. In any case, Harpers offered a contract so unfavorable that it may actually have been meant as a form of rejection. Further fueling Melville’s ire was reading the uncomprehending reviews of Moby-Dick while he was in New York. Parker further reasons that Melville may have shown the original, shorter manuscript to Everett Duyckinck, who condemned the sexual content as immoral. In frustration and retaliation, Parker concludes, Melville, perhaps in two or three batches, may only then have added the sections dealing with Pierre’s literary career, especially the chapter “Young America in Literature,” which describes publishers and critics in scathing terms. These additions undermined the structure of the novel and muddied the characterization of Pierre, who Melville had not originally been intended to be an author. 
Parker prepared an 1995 edition of the book which demonstrates what the original might have been like by removing the sections which present Pierre as an author, notably Books XVII, XVIII, XXII, with shorter deletions elsewhere. The Melville scholar John Bryant praised this edition's pictures by Maurice Sendak, which present Pierre as a "full-blown adolescent: muscular, ecstatic, desperate, devoted, and lonely; he is the man-child invincible.” Bryant points out that Sendak's earlier children’s book Pierre was written with Melville in mind.