Starr first accepted the position in 1997 ago but changed his mind after he was criticized for abandoning the Whitewater investigation into the Clintons' real estate dealings.
The appointment, which was to be officially announced Tuesday, followed a more than six-month national search, said Brad Cheves, the university's vice president for advancement and public affairs.
Starr, a longtime guest lecturer at Malibu-based Pepperdine, was acting as independent counsel when he led the Lewinsky investigation, which ended with the first impeachment of a president since 1868.
He has since has argued cases before the U.S. Supreme Court and taught at New York University Law School.
Starr, a partner at Kirkland & Ellis in Washington and former federal appeals court judge and U.S. solicitor general, will begin work at Pepperdine on August 1.