Having acquired a taste for literature in his father's book-shop, he sought and obtained admission into the order of the Jesuits in around 1662 (when he was 16). In Paris, where he went to study theology. He ultimately became librarian of the Lycée Louis-le-Grand in 1683, and he died there.
His first published work was an edition of Themistius (1684), which included no fewer than thirteen new orations. On the advice of Jean Garnier (1612–1681) he undertook to edit the Natural History of Pliny for the Dauphin series, a task which he completed in five years. Aside from editorial work, he became interested in numismatics, and published several learned works on this subject, all marked by a determination to be different from other interpreters. His works on this topic include: Nummi antiqui populorum et urbium illustrati (1684), Antirrheticus de nummis antiquis coloniarum et municipiorum (1689), and Chronologia Veteris Testamenti ad vulgatam versionem exacta et nummis illustrata (1696).
Hardouin was appointed by the ecclesiastical authorities to supervise the Conciliorum collectio regia maxima (1715); but he was accused of suppressing important documents and including apocryphal ones, and by the order of the parlement of Paris (then in conflict with the Jesuits) the publication of the work was delayed. After his death a collection of works Opera varia appeared in Amsterdam 1733.
It is, however, as the originator of a variety of eccentric theories that Hardouin is now best remembered. The most remarkable, contained in his Chronologiae ex nummis antiquis restitutae (1696) and Prolegomena ad censuram veterum scriptorum, was to the effect that, with the exception of the works of Homer, Herodotus and Cicero, the Natural History of Pliny, the Georgics of Virgil, and the Satires and Epistles of Horace, all the ancient classics of Greece and Rome were spurious, having been manufactured by monks of the 13th century, under the direction of a certain Severus Archontius by whom he might have meant Frederick II. He denied the genuineness of most ancient works of art, coins and inscriptions, and declared that the New Testament was originally written in Latin, as he underlined with good reasoning in his short work Prolegomena which appeared in the year he died, 1729. The Prolegomena were translated by Edwin Johnson and published by Angus and Robertson, Sydney 1909, with a noteworthy preface of Edward A. Petherick.
Although Hardouin has been called "pathological", he was only an extreme example of a general critical trend of his time, following authors like Baruch Spinoza, Thomas Hobbes or Jean Daillé, who had started to identify and discard mistaken attributions or datings of medieval documents or Church writings 
Hardouin also perceived anachronisms in Dante's Purgatorio, in notes published in Paris 1727, which was edited with an English commentary in London 1847 by C. F. Molini. The historian Isaac-Joseph Berruyer had his Histoire du peuple de Dieu condemned for having followed this theory, which has a modern heir in the Russian mathematician Anatoly Timofeevich Fomenko, whose conclusions being based on proprietary methods of statistical textual analysis and computational astronomy are even more radical, but considered to be pseudoscientific.
- Augustin de Backer, Bibliothèque des écrivains de la Compagnie de Jesus (1853).
- English Translation of The Prolegomena
- Meyers Konversations-Lexikon, Leipsic 1887, 4th ed., t. 8: Jean Hardouin
- Harold Love: Attributing Authorship (Cambridge University Press, 2002), pp 186-188
- Hardouins Prolegomena in englischer Übersetzung by Uwe Topper, in CronoLogo (2014)
- The Oxford History of Historical Writing (Oxford University Press, 2012), p. 270
- Hardouins Zweifel zu Dante by Uwe Topper, in CronoLogo, 2011