В 1992—1996 годы — научный сотрудник факультета религиоведения Утрехтского университета.
В 1995 году получил докторскую степень в Утрехтском университете защитив диссертацию «Религия Нового века и западная культура: эзотеризм в зеркале секулярного мышления» (англ.New Age Religion and Western Culture: Esotericism in the Mirror of Secular Thought).
В 1996—1999 годы работал научным сотрудником в Нидерландской ассоциации научных исследований, включая проведение исследований в Париже.
Hanegraaff W. J., Bouthoorn R. M. Lodovico Lazzarelli (1447-1500): The Hermetic Writings and Related Documents. — Tempe: Arizona Center for Medieval and Renaissance Studies, 2005.
Hanegraaff W. J. Aries Book Series: Texts and Studies in Western Esotericism. — Leiden & Boston: Brill, 2006.
Hanegraaff W. J. Swedenborg, Oetinger, Kant: Three Perspectives on the Secrets of Heaven. — West Chester: The Swedenborg Foundation, 2007. — (Swedenborg Studies Series, no. 18). — ISBN 978-0-87785-321-3.
Hanegraaff W. J. Giovanni da Correggio's De Quercu, sive de lapide philosophico // L.M. Principe (Ed.), Chymists and Chymistry : Studies in the History of Alchemy and Early Modern Chemistry. — Sagamore Beach: Watson Publishing International LLC, 2007. — P. 101—112.
Hanegraaff W. J. The Trouble with Images: Anti-Image Polemics and Western Esotericism' // O. Hammer & K. von Stuckrad (Eds.), Polemical Encounters: Esotericism and its Others (pp. ). — Leiden / Boston: Brill, 2007. — P. 107—136.
Hanegraaff W. J. 'The New Age Movement and Western Esotericism' // D. Kemp & J. R. Lewis (Eds.), Handbook of New Age. — Leiden / Boston: Brill, 2007. — P. 25—50.
Hanegraaff W. J. Fiction in the Desert of the Real: Lovecraft's Cthulhu Mythos' // Aries[англ.]. — 2007. — Vol. 7 (1). — P. 85—109.
Hanegraaff W. J. Hermetische tradities en de natuurwetenschappen: Tussen beeldvorming en complexiteit // F.J. Meijman, S. Snelders & O. de Wit (Eds.), Leonardo voor het publiek: Een geschiedenis van de wetenschaps- en techniekcommunicatie. — Amsterdam: VU University Press & Da Vinci Institute. — P. 295—305).
Hanegraaff W. J. Swedenborg aus der Sicht von Kant und der akademischen Kantforschung // F. Stengel (Ed.), Kant und Swedenborg: Zugänge zu einem umstrittenen Verhältnis (Hallesche Beiträge zur europäischen Aufklärung, 38). — Tübingen: Niemeyer, 2008. — P. 157—172.
Hanegraaff W. J., Kripal J.J.[англ.]. Introduction: things we do not talk about // W.J. Hanegraaff & J. J. Kripal[англ.] (Eds.), Hidden intercourse: eros and sexuality in the history of Western esotericism (Aries book series, 7). — Leiden / Boston: Brill, 2008. — P. ix-xxii.
Hanegraaff W. J. Swedenborg’s magnum opus: [introduction] // E. Swedenborg & L. Hyatt Cooper (Eds.), A disclosure of secrets of heaven contained in Sacred Scripture or the Word of the Lord : here first those in Genesis, together with amazing things seen in the world of spirits & in the heaven of angels. - Vol. 1: Genesis 1-8 (The New Century edition of the works of Emanuel Swedenborg). — West Chester: The Swedenborg Foundation, 2008. — P. 63—129.
Hanegraaff W. J. La nascita dell’esoterismo dallo spirito del Protestantesimo // A. Grossato (Ed.), Forme e correnti dell’esoterismo occidentale. — Milano: Medusa, 2008. — С. 125—144.
Hanegraaff W. J. Under the mantle of love: the mystical eroticisms of Marsilio Ficino and Giordano Bruno // W.J. Hanegraaff & J. J. Kripal[англ.] (Eds.), Hidden intercourse: eros and sexuality in the history of Western esotericism (Aries book series, 7). — Leiden / Boston: Brill, 2008. — С. 175—207.
Hanegraaff W. J. New Age religion // L. Woodhead, H. Kawanami & C. Partridge (Eds.), Religions in the modern world : traditions and transformations. — London / New York: Routledge, 2009. — Т. 4 (1). — С. 339—356. — ISSN1872-5473.
Hanegraaff W. J. Ten years of studying and teaching western esotericism // W.J. Hanegraaff & J. Pijnenburg (Eds.), Hermes in the Academy: ten years' study of western esotericism at the University of Amsterdam. — Amsterdam: Amsterdam University Press[англ.], 2009. — С. 17—29.
Hanegraaff W. J. The seminal essence of divinity: Swedenborg’s understanding of Jesus Christ // O. Hammer (Ed.), Alternative Christs. — Cambridge: Cambridge University Press, 2009. — С. 131—149. — ISSN1872-5473.
Hanegraaff W. J. The pagan who came from the East: George Gemistos Plethon and Platonic orientalism // W.J. Hanegraaff & J. Pijnenburg (Eds.), Hermes in the Academy: ten years' study of western esotericism at the University of Amsterdam. — Amsterdam: Amsterdam University Press[англ.], 2009. — С. 33—49. — ISSN1872-5473.
Hanegraaff W. J. The beginnings of occultist Kabbalah: Adolphe Franck and Eliphas Lévi // B. Huss, M. Pasi & K. von Stuckrad (Eds.), Kabbalah and modernity: interpretations, transformations, adaptations (Aries book series, 10). — Leiden: Brill, 2010. — С. 107—128.
Hanegraaff W. J. Philosophy’s shadow: Jacob Brucker and the history of thought // R. Bod, J. Maat & T. Weststeijn (Eds.), The making of the humanities. — Amsterdam: Amsterdam University Press[англ.], 2010. — Т. 1: Early Modern Europe (2). — С. 367—384.
Hanegraaff W. J. Western esotericism in Enlightenment historiography: the importance of Jacob Brucker // A.B. Kilcher (Ed.), Constructing tradition: means and myths of transmission in western esotericism. — Leiden: Brill, 2010. — Т. 11: Aries Book Series. — С. 91—111.
Hanegraaff W. J. The unspeakable and the law: esotericism in Anton Webern and the Second Viennese School // L. Wuidar (Ed.), Music and esotericism. — Leiden: Brill, 2010. — Т. 9: Aries Book Series. — С. 329—353.
Hanegraaff W. J. The Platonic frenzies in Marsilio Ficino // J. Dijkstra, J. Kroesen & Y. Kuiper (Eds.), Myths, martyrs, and modernity: studies in the history of religions in honour of Jan N. Bremmer (Numen book series, 127). — Leiden: Brill, 2010. — С. 553—568.
Hanegraaff W. J. And end history. And go to the stars': Terence McKenna and 2012 // C.M. Cusack & C. Hartney (Eds.), Religion and retributive logic: essays in honour of professor Garry W. Trompf (Numen book series, 126). — Leiden: Brill, 2010. — С. 291—312.
Hanegraaff W. J. Will-Erich Peuckert and the light of nature // A. Versluis, C. Fanger, L. Irwin & M. Phillips (Eds.), Esotericism, religion, and nature (Studies in esotericism series / Association for the Study of Esotericism, 2). — Minneapolis: North American Academic Press, 2010. — С. 281—305.
Hanegraaff W. J. Magnetic gnosis: somnambulism and the quest for absolute knowledge // A.B. Kilcher & P. Theisohn (Eds.), Die Enzyklopädik der Esoterik: Allwissenheitsmythen und universalwissenschaftliche Modelle in der Esoterik der Neuzeit. — Paderborn: Wilhelm Fink, 2010. — С. 259—276.
Hanegraaff W. J. Ayahuasca groups and networks in the Netherlands: a challenge to the study of contemporary religion // B.C. Labate & H. Jungaberle (Eds.), The Internationalization of Ayahuasca. — Zürich: Lit Verlag, 2011. — Т. 2 (Critical concepts in social studies). — С. 85—103.
Hanegraaff W. J.Kabbalah in Gnosis magazine (1985-1999) // B. Huss (Ed.), Kabbalah and contemporary spiritual revival (Goldstein-Goren library of Jewish thought, 14). — Beer-Sheva: Ben-Gurion University of the Negev Press, 2011. — С. 251—266.
Hanegraaff W. J. Joseph Ennemoser and magnetic historiography // Politica Hermetica. — 2011. — Vol. 25. — P. 65—83.
Ханеграаф В. Я. Западный эзотеризм: Следующее поколение // Aliter. — 2013. — № 1. — С. 7—23.
Hanegraaff W. J. Entheogenic esotericism // E. Asprem & K. Granholm (Eds.), Contemporary esotericism (Gnostica: texts and interpretations). — Sheffield: Equinox, 2012. — С. 392—409.
Hanegraaff W. J. Western esotericism: the next generation // Mystic and esoteric movements in theory and practice: fifth international conference: history and discourse: historical and philosophical aspects of the study of esotericism and mysticism. — St. Petersburg: Russian Christian Academy for Humanities, 2012. — С. 113—129.
Hanegraaff W. J. The Notion of "Occult Sciences" in the Wake of the Enlightenment // M. Neugebauer-Wölk, R. Geffarth & M. Meumann (Eds.), Aufklärung und Esoterik: Wege in die Moderne (Hallesche Beiträge zur Europäischen Aufklärung). — Berlin: Walter de Gruyter. — P. 73—95.
Hanegraaff W. J.Hermetism // Oxford Guide to the Historical Reception of Augustine (англ.) / K. Pollmann (Ed.). — Oxford: Oxford University Press, 2013. — Vol. 2. — P. 1135—1139.
Hanegraaff W. J. Jan Assmann // R. Celikates, R. Gabriëls, J.F. Hartle, P. Lemmens & T. Lijster (Eds.), De nieuwe Duitse filosofie: denkers en thema's voor de 21e eeuw. — Amsterdam: Boom, 2013. — P. 480—486.
Ганеграаф В. Мрії про теологію та реальність християнства // Філософська думка : Український науково-теоретичний часопис. — 2013. — № 3. — С. 92—116.
Научная редакция
Female Stereotypes in Religious Traditions / ed. Wouter Hanegraaff, Ria Kloppenborg. — Leiden: Brill, 1995. — ISBN 978-90-04-10290-3.
Gnosis and Hermeticism from Antiquity to Modern Times / ed. Wouter Hanegraaff, Roelof van den Broek, Wouter Hanegraaff. — Albany: State University of New York Press, 1998.
Western Esotericism and the Science of Religion / ed. Wouter Hanegraaff, Antoine Faivre. — Peeters, 1998.
Ésotérisme, gnoses & imaginaire symbolique: Mélanges offerts à Antoine Faivre / ed. Wouter Hanegraaff, Richard Caron, Joscelyn Godwin & Jean-Louis Vieillard-Baron. — Peeters, 2001.
Dictionary of Gnosis and Western Esotericism / ed. Wouter Hanegraaff, Antoine Faivre, Roelof van den Broek, Jean-Pierre Brach. — Leiden: Brill, 2005. — ISBN 978-90-04-15231-1.
Hidden Intercourse: Eros and Sexuality in the History of Western Esotericism / ed. Wouter Hanegraaff, Jeffrey J. Kripal[англ.]. — Leiden: Brill, 2008.
Hermes in the Academy:Ten Years' Study of Western Esotericism at the University of Amsterdam / ed. Wouter Hanegraaff, Joyce Pijnenburg. — Amsterdam: Amsterdam University Press[англ.], 2009.
Hidden Intercourse: Eros and Sexuality in the History of Western Esotericism / ed. Wouter Hanegraaff, Jeffrey J. Kripal[англ.]. — Leiden / Boston: Brill, 2008.
Hanegraaff W. J. "Everybody is Right": Frank Visser's Analysis of Ken Wilber. [Review of the book Ken Wilber: Denken als passie] // integralworld. — 2006.
Hanegraaff W. J. "Everybody is Right": Frank Visser's Analysis of Ken Wilber. [Review of the book Ken Wilber: Denken als passie] // integralworld. — 2007.
Hanegraaff W. J. Review of the book Hermetism from Late Antiquity to Humanism / La tradizione Ermetica dal mondo tardo-antico all'umanesima: Atti del Convegno internazionale di studi, Napoli, 20-24 novembre 2001 // Aries[англ.]. — 2007. — Т. 7(2). — С. 227—229.
Hanegraaff W. J. Review of the book Études d’histoire de l’ésotérisme: mélanges offerts à Jean-Pierre Laurant pour son soixante-dixième anniversaire // Aries[англ.]. — 2009. — Vol. 9(2). — P. 290—292.
Hanegraaff W. J. Review of the book An Introduction to Western Esotericism: Essays in the Hidden Meaning of Literature, Groups, and Games // Nova Religio: Journal of Alternative and Emergent Religions. — 2012. — Vol. 16(3). — P. 125—126.
Hanegraaff W. J. Review of the book Aufklärung und Esoterik: Rezeption, Integration, Konfrontation // Aries[англ.],. — 2012. — Vol. 12(2). — P. 181—185.
Hanegraaff W. J. Review of the book Locations of knowledge in medieval and early modern Europe: esoteric discourse and Western identities // Nederlands Theologisch Tijdschrift. — 2012. — Vol. 66(1). — P. 72—73.
Научно-популярные труды
Hanegraaff W. J. Geven in plaats van verkopen // J. Baijens (Ed.), Het beste idee van 2013. — Tilburg: De Wereld, 2013. — P. 170—171).
Hanegraaff W. J. Schöpfung und Zerstörung: Bemerkungen zum Geheimnis der Esoterikforschung // Gnostika. — Vol. 50. — P. 20—23.
Hanegraaff W. J. Per aspera ad fontes. Pentagram. — 2012. — Vol. 34 (1). — P. 18—25.
Hanegraaff, W. New Age Religion and Western Culture: Esotericism in the Mirror of Secular Thought (англ.). — Leiden: Brill, 1998. — ISBN 978-9004106956.