Mahant Sundar Das was booked following a court order on October 2, for the crime allegedly committed three years ago, they said.
He has been charged with one count of assault or criminal force on a woman with intent to outrage her modesty, one count of sexual harassment and one count of criminal intimidation, Jatin Narwal, deputy commissioner of police (north), said.
"The matter is under investigation," Narwal said.
Das runs an ashram in Sabzi Mandi area where the victim used to visit along with her family. The woman in her complaint alleged that Das molested her in November 2014 and threatened her against reporting the matter to the police.
The complainant later approached a court, which ordered the police to register a case against the accused.
No arrest has been made in the case so far, the police added.