Gulliver's Travels was quite a success in its time. The first printing sold out immediately and the book was translated into French, Dutch, and German. It appealed to people from all social classes and ages, and readers thought the book was a humorous adventure tale, suitable even for children to read (the separate category of books especially for children did not come about until a generation after Swift's death). Gulliver was perceived as a "happy fellow." (Note, however, that the original editor of the work had toned down some of the satire, which was not restored to the text until 1735.) By the end of the 1700s, however, people were beginning to see past the fun adventure plot and become aware of Swift's hidden messages. Many were shocked by the negativity of the book and condemned it. Writer William Makepeace Thackeray said the message of the book was "horrible, shameful, blasphemous … filthy in word, filthy in thought" and "obscene," and certainly proof that Jonathan Swift was "about the most wretched being in God's world."

Sir Walter Scott obviously thought Gulliver's Travels had some merit or he wouldn't have published a collection of Swift's works in 1814. He noted that the work was "unequalled for the skill with which [the narrative] is sustained, and the genuine spirit of satire of which it is made the vehicle." He also declared, however, that the book was "severe, unjust and degrading" and dismissed early fans as people who, like Swift, had obviously been in a "state of gloomy misanthropy." Swift was accused again and again of being a bitter misanthrope who hated mankind, a pessimist who wouldn't acknowledge the good qualities of human beings. For a time only Part III was considered acceptable reading, and Part IV was considered exceptionally offensive right up through the 1800s. In 1889, Edmund Gosse urged "decent" people to avoid reading Part IV because of the "horrible foulness of this satire." And in 1882 Leslie Stephen speculated that the "oppressive" tone of "misanthropy" in Parts III and IV must have been the result of Swift's bitterness over ill health and dashed ambitions and suggested that readers skip them altogether. His contemporary, Churton Collins, said the book had "no moral, no social, no philosophical purpose." The novel's controversial messages about politics and the nature of man even led to censorship. In later editions, right up until 1899, the Lindalinian revolt at the end of Part III was excised because it was (probably correctly) interpreted as a symbol of the righteousness of a potential Irish revolt.

However, despite the early controversies, critics over the years have come to hail Gulliver's Travels as the greatest satire by the greatest prose satirist in the English language. An early fan, William Hazlitt, said in 1818 that Swift's object had not been to spew venom but to "strip empty pride and grandeur" and "to show men what they are, and to teach them what they ought to be." Novelist Aldous Huxley (author of the antiutopian novel Brave New World) said in the early twentieth century that Swift was an incurable sentimentalist and romantic who resented reality. Indeed, most critics today think that Swift has been misunderstood, probably since many readers have mistakenly assumed that Gulliver, who certainly is a misanthrope at the end, is a mouthpiece for Swift.

Swift's bitterness, contemporary critics argue, is not the product of insanity or illness but the inevitable result of a caring, compassionate, religious man who had seen the worst side of human nature. As a young man, Swift had tried to serve his country through work with political parties, and wanted to serve in the Church of England, but petty politics destroyed his and his friends' plans and drove them into exile. In Ireland, Swift saw the greed of the British drive a country of people to poverty and desperation. He tried, in Gulliver's Travels, to alert people to the ugliness of human behavior. Yet at the same time, he hoped that the novel, and his other works, would rouse them to strive to do better. Swift denied that he hated people. He wrote, "I have ever hated all Nations, professions, and Communityes and all my love is toward individuals." His inclusion of the kindly, charitable Captain Pedro de Mendez in the end of the book supports Swift's claim that he believed there are good, admirable individuals in the world.

As for the novel itself, critics have generally agreed that Part III is the weakest and least unified of the four sections, possibly because it was the last written. Some have claimed the fourth section of Part III is an unnecessary departure from the major themes of the book, focusing as it does on Swift's fears of growing old and senile (which, in fact, he did). Also, in Part III, Gulliver is merely an observer, which makes the voyage less engaging than the others.

Critics have agreed about what Swift was satirizing in each of the first three voyages. They have disagreed, however, on how to interpret the fourth voyage. Do the Houyhnhnm and Yahoos represent the dual nature of humanity, good and evil? Or do the Houyhnhnm represent Swift's view that utopian thinkers are foolish in their attempts to imagine a perfect human society? Critics since 1950 have generally agreed that the Houyhnhnm are symbols of unattainable human perfection which can be the ideal we strive for, even if we fall short, and the Yahoos represent how far into ugliness we can fall if we lose sight of our ideals.

Critics have suggested that Swift intended the novel to be both an attack on mankind and its follies and a honest assessment of mankind's positive and negative qualities. It is also considered a critique of the greatest moral, philosophical, scientific, and political ideas of Swift's time. The greatest and most lasting accomplishment of Gulliver's Travels may be its ability to encourage readers of any society at any time to raise important questions about mankind's limitations, how we can structure our institutions to bring out the best in people, and what it means to be human.