David Boyd, 54, of Chesterton Court, Stockton-on-Tees, did not enter a plea to the allegation at South Tyneside Magistrates’ Court this morning.
Seven-year-old Nikki vanished after leaving her grandparents’ flat in the Wear Garth area of the city on Wednesday 7 October 1992.
Nikki’s body was later found in the then derelict Old Exchange building a few hundred yards away, after her shoes were spotted outside.
She had been stabbed 37 times.
No application for bail was made and Boyd was remanded in custody.
He will appear tomorrow at Newcastle Crown Court.
Prosecutor Niamh Reading told the hearing: “Because of the nature of this offence, it can only be heard at the crown court.
Remanding Boyd into custody, District Judge Paul Currer told him the allegation was so serious it must be heard at a crown court.