The early eighteenth-century Deist scholar John Toland used the murder of Hypatia as the basis for the anti-Catholic tract, Hypatia: Or the History of a most beautiful, most vertuous, most learned, and every way accomplish'd Lady; who was torn to pieces by the Clergy of Alexandria, to gratify the pride, emulation, and cruelty of their Archbishop, commonly, but undeservedly, stil'd St. Cyril. In order to portray Hypatia's death in the worst possible light, Toland changed the story and invented elements not found in any of the ancient sources. In 1721, Thomas Lewis wrote a response defending Cyril entitled The History of Hypatia, a most Impudent School-Mistress of Alexandria: Murder'd and torn to Pieces by the Populace, in Defence of Saint Cyril and the Alexandrian Clergy from the Aspersions of Mr. Toland. Lewis rejected Damascius's account as unreliable out of hand on account of the fact that its author was "a heathen" and then proceeded to argue that Socrates Scholasticus was "a Puritan", who was consistently biased against Cyril.

Voltaire, in his Examen important de Milord Bolingbroke ou le tombeau de fantisme (1736) interpreted Hypatia as a believer in "the laws of rational Nature" and "the capacities of the human mind free of dogmas" and described her death as "a bestial murder perpetrated by Cyril's tonsured hounds, with a fanatical gang at their heels". Later, in an entry for his Dictionnaire philosophique (1772), Voltaire again portrayed Hypatia as a freethinking deistic genius brutally murdered by ignorant and misunderstanding Christians. Most of the entry ignores Hypatia herself altogether and instead deals with the controversy over whether or not Cyril was responsible for her death. Voltaire concludes with the snide remark that "When one strips beautiful women naked, it is not to massacre them."

In nineteenth century European literary authors spun the legend of Hypatia as part of neo-Hellenism, a movement that romanticised ancient Greeks and their values. Interest in the "literary legend of Hypatia" began to rise. Diodata Saluzzo Roero's 1827 Ipazia ovvero delle Filosofie suggested that Cyril had actually converted Hypatia to Christianity, and that she had been killed by a "treacherous" priest.

At the same time, European Philosophers and Scientists described Hypatia as the last representative of science and free inquiry before a "long medieval decline". In 1843, German authors Soldan and Heppe argued in their highly influential History of the Witchcraft Trials that Hypatia may have been, in effect, the first famous "witch" punished under Christian authority (see witch-hunt).

In his 1852 Hypatie and 1857 Hypathie et Cyrille, French poet Charles Leconte de Lisle portrayed Hypatia as the epitome of "vulnerable truth and beauty". Leconte de Lisle's first poem portrayed Hypatia as a woman born after her time, a victim of the laws of history. His second poem reverted back to the eighteenth-century Deistic portrayal of Hypatia as the victim of Christian brutality, but with the twist that Hypatia tries and fails to convince Cyril that Neoplatonism and Christianity are actually fundamentally the same. Charles Kingsley's 1853 novel Hypatia; Or, New Foes with an Old Face was originally intended as a historical treatise, but instead became a typical mid-Victorian romance with a militantly anti-Catholic message, portraying Hypatia as a "helpless, pretentious, and erotic heroine" with the "spirit of Plato and the body of Aphrodite."

Hypatia's death shocked the empire and transformed her into a "martyr for philosophy", leading Future Neoplatonists such as Damascius to become increasingly fervent in their opposition to Christianity. During the Middle Ages, Hypatia was co-opted as a symbol of Christian virtue and scholars believe she was part of the basis for the legend of Saint Catherine of Alexandria. During the Age of Enlightenment, she became a symbol of opposition to Catholicism. In the nineteenth century, European literature, especially Charles Kingsley's 1853 novel Hypatia, romanticized her as "the last of the Hellenes". In the twentieth century, Hypatia became seen as an icon for women's rights and a precursor to the feminist movement. Since the late twentieth century, some portrayals have associated Hypatia's death with the burning of the Library of Alexandria, despite the historical fact that the library no longer existed during Hypatia's lifetime.

As an Astronomer Hypatia was honoured when 238 Hypatia, a main belt asteroid discovered in 1884, was named for her. The Lunar crater Hypatia was also named for her, in addition to craters named for her Father Theon. The 180 km Rimae Hypatia are located north of the crater, one degree south of the equator, along the Mare Tranquillitatis.

Hypatia wrote a commentary on Diophantus's thirteen-volume Arithmetica, which had been written c. 250. It set out more than 100 mathematical problems, for which solutions are proposed using algebra. It was long believed that this commentary had been lost, but the nineteenth-century scholar Paul Tannery deduced that parts of it had actually survived, interpolated into Diophantus's original text, of which only volumes 1-6 have survived. Sir Thomas Heath published the first English translation of the surviving portion of the Arithmetica in 1885. Heath argued that surviving text of Arithmetica is actually a redaction produced by Hypatia to aid her students. Hypatia used an unusual algorithm for division (in the then-standard sexagesimal numeral system), making it easy for scholars to pick out which parts of the text she had written.

Kingsley's novel was tremendously popular; it was translated into several European languages and remained continuously in print for the rest of the century. It promoted the romantic vision of Hypatia as "the last of the Hellenes" and was quickly adapted into a broad variety of stage productions, the first of which was a play written by Elizabeth Bowers, performed in Philadelphia in 1859, starring the Writer herself in the titular role. On 2 January 1893, a much higher-profile stage play adaptation Hypatia, written by G. Stuart Ogilvie and produced by Herbert Beerbohm Tree, opened at the Haymarket Theatre in London. The title role was initially played by Julia Neilson, and it featured an elaborate musical score written by the Composer Hubert Parry. The novel also spawned works of visual art, including an 1867 portrait of Hypatia as a young woman by the early Photographer Julia Margaret Cameron and an 1885 painting by Charles william Mitchell showing a nude Hypatia standing before an altar in a church.

In the twentieth century Hypatia's life and death was cast in the light of women's rights and she was adopted by feminists. The author Carlo Pascal claimed in 1908 that her murder was an anti-feminist act and brought about a change in the treatment of women, as well as the decline of the Mediterranean civilisation in general. Dora Russell, the wife of Bertrand Russell, published a book on the inadequate education of women and inequality with the title Hypatia or Woman and Knowledge in 1925. The prologue explains why she chose the title: "Hypatia was a university lecturer denounced by Church dignitaries and torn to pieces by Christians. Such will probably be the fate of this book."

The thirteenth and final episode of Carl Sagan's 1980 PBS series Cosmos: A Personal Voyage relates a heavily fictionalized retelling of Hypatia's death, which results in the "Great Library of Alexandria" being burned by militant Christians. In actuality, though Christians led by Theophilus did indeed burn the Serapeum in 391 AD, the Library of Alexandria had already ceased to exist in any recognizable form centuries prior to Hypatia's birth.

As an intellectual woman, Hypatia became a role model for modern intelligent women and two feminist journals were named after her: the Greek journal Hypatia: Feminist Studies was launched in Athens in 1984, and Hypatia: A Journal of Feminist Philosophy was launched in the United States in 1986. In the United Kingdom, the Hypatia Trust has compiled a library and archive of feminine literary, artistic and scientific work since 1996. An extension of the trust has established the Hypatia-in-the-Woods retreat in Washington State, where artistic, Business and academic women can spend time to work on projects.

Hypatia's life continues to be fictionalized by authors in many countries and languages. In Umberto Eco's 2002 novel Baudolino, the hero falls in love with a half-satyr, half-woman, who is descended from a group of Hypatia's young female disciples, who fled after their teacher's murder. These disciples set up a female-only community who "tried to keep alive what they had learned from their mistress... [living] apart from the world, to rediscover what Hypatia had really said." All the women, who reproduce by "fecundation" with satyrs, are named Hypatia and are collectively known as "hypatias". Charlotte Kramer's 2006 novel Holy Murder: the Death of Hypatia of Alexandria portrays Cyril as an archetypal villain without an ounce of good. Hypatia is repeatedly described as brilliant and beloved and she humiliates Cyril by demonstrating that she knows more about the Christian scriptures than he does. Ki Longfellow's novel Flow Down Like Silver (2009) invents an elaborate backstory for why Hypatia first started teaching. Youssef Ziedan's novel Azazeel (2012) describes Hypatia's brutal murder through the eyes of the monk Hypa, who witnesses the incident. In The Plot to Save Socrates (2006) by Paul Levinson and its sequels Unburning Alexandria (novelette, 2008; novel 2013) and Chronica, Hypatia turns out to have been a time-traveler from the twenty-first century United States.

The 2009 movie Agora, directed by Alejandro Amenábar and starring Rachel Weisz as Hypatia, is a heavily fictionalized dramatization of Hypatia's final years. The film, which was intended to criticize contemporary Christian fundamentalism, has had wide-ranging impact on the popular conception of Hypatia. Unlike previous fictional adaptations, Agora emphasizes Hypatia's astronomical and mechanical studies rather than her philosophy, portraying her as "less Plato than Copernicus". It also, more than any other previous portrayal, emphasizes the restrictions imposed on women by the early Christian church. In one scene, Hypatia is sexually assaulted by one of her father's slaves, who has recently converted to Christianity, and, in another scene, Cyril reads a verse from 1 Timothy 2:8-12 forbidding women from teaching. Near the end of the film, Synesius warns Orestes that he must abandon his friendship with Hypatia in order to retain his faith as a Christian. The film also portrays Cyril and his monks as swarthy, bearded men with covered heads clad in tattered black clothing, resembling media portrayals of the Taliban.

Ari Belenkiy describes Hypatia's astronomical work as pivotal for the politics of the region, focusing on controversies related to observations of the equinox and the timing of festivals, ultimately serving to highlight errors in Ptolemy's work and the need for independent observation. In two consecutive works (2010, 2016) Belenkiy proposed an astronomical-calendrical paradigm for Hypatia's murder. Comparing two principal sources on Hypatia, of Socrates Scholasticus and Philostorgius, Belenkiy suggests that Hypatia carried out equinoctial observations in 414-415, initiated on the request of governor Orestes. This could have been the litmus test of who was right in the conflicts over the 414 Easter day waged by Cyril, the Bishop of the Alexandrian Church, with the local Jewish and Novatian communities. Hypatia's success in establishing the correct day of the vernal equinox could undermine the Alexandrian Church's authority in the timing of Easter, as it used equinoctial computations based on Ptolemy's Syntaxis (Almagest).

From 382 – 412, the bishop of Alexandria was Theophilus. Theophilus was militantly opposed to Iamblichean Neoplatonism and, in 391, he demolished the Serapeum. Despite this, Theophilus tolerated Hypatia's school and seems to have regarded Hypatia as his ally. Theophilus supported the bishopric of Hypatia's pupil Synesius, who describes Theophilus in his letters with love and admiration. Theophilus also permitted Hypatia herself to establish close relationships with the Roman prefects and other prominent political Leaders. Partly as a result of Theophilus's tolerance, Hypatia became extremely popular with the people of Alexandria and exerted profound political influence.

It is possible that Hypatia may have edited her father's commentary on Euclid's Elements. Her Father mentions the manuscript as being "the recension of my philosopher-daughter Hypatia", though it is not clear whether she edited or revised her father’s work, or indeed authored any part of it. Theon also edited the existing version of Euclid's Elements, correcting scribal errors that had been made over the course of nearly 700 years of copying, and Hypatia is believed to have assisted him. Theon and Hypatia's edition of Euclid's Elements became the most widely-used edition of the textbook for centuries and almost totally supplanted all other editions.