Ray, 46, turned himself in to police Thursday and faces a June 12 court date on the misdemeanor stalking charge.
Ray, a lawyer with the Parsippany, N.J., firm Kelley Drye & Warren LLP, is accusing of persistently e-mailing and knocking on the door of his 40-year-old ex-girlfriend for months after she ended their relationship, The Washington Post reported Saturday.
Ray, who took over for Independent Counsel Kenneth Star in October 1999, investigated Clinton's affair with White House Intern Monica Lewinsky as well as the Whitewater land deal in Arkansas.
The one-time federal prosecutor, in December 2000, began the deal that allowed Clinton to avoid indictment on perjury and obstruction of justice charges, the newspaper reported.
Ray's final March 2002 report was highly critical of Clinton's conduct.
Ray could not be reached for comment on the stalking charge, the Post said.
2014: The Year in Music [PHOTOS]