Elst was born into a Flemish Catholic family but he rejects Roman Catholicism and instead calls himself a “secular humanist”. 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 PhD in Asian Studies from Leuven. His doctoral dissertation on Hindu revivalism was published as Decolonizing the Hindu Mind.