Elst was born to a Flemish Catholic family. Some of his family members were Christian missionaries. He graduated in Indology, Sinology and Philosophy at the Catholic University of Leuven. Around that time, Elst became interested in Flemish nationalism. Between 1988 and 1992, Elst was at the Banaras Hindu University. In 1999, he received a Ph.D. from the Catholic University of Leuven. His doctoral dissertation on Hindu revivalism was published as Decolonizing the Hindu Mind.
Elst, known for his support for the Out of India theory related to Indo-Aryan migration, has also written about multiculturalism, language policy issues, ancient Chinese philosophy and history, and comparative religion. Elst became identified with Hindutva politics during the 1990s, following his support for the Bharatiya Janata Party’s position on the Ram Janmabhoomi temple in Ayodhya and in parallel with the BJP’s rise to prominence on the national stage.