A spokeswoman for the Manhattan prosecutor's office says the Reverend David Ajemian of the Archdiocese of Boston was arrested while trying to enter a taping session of NBC's "Late Night" last week.
He's accused of writing threatening notes on parish letterhead and contacting O'Brien's parents.
Court papers say the suspect referred to himself as "your priest stalker" in one note, and complained of not being allowed to see an earlier taping of the show.
The note asked: "Is this the way you treat your most dangerous fans?" It, and others, were signed "Padre."
The priest, who's on leave, could face up to a year in prison if convicted of aggravated harassment and stalking.
O'Brien is not commenting.