Mertz is charged with first-degree murder, first-degree felony murder and first-degree aggravated sexual assault. If convicted he faces 30 years to life behind bars.
Gloucester County Prosecutor Sean Dalton said Whipkey was at the Adelphia night club in Deptford on May 24, 2002 and at some point encountered Mertz after the club closed.
The prosecutor said Mertz then sexually assaulted and killed Whipkey, then left her body in a wooded area near the Westwood Motor Lodge, where Mertz was living the time.
Whipkey's body was found 24 hours later by a man on a newspaper delivery route. She had been stabbed numerous times in the throat, head, chest, abdomen and legs.
Whipkey was the mother of a four-year-old girl.
"Today I stand here grateful. We've waited a long time for this day," said Elizabeth McCool, Whipkey's mother. "I could not have received a better gift this Christmas than to see the man responsible for Jen's murder brought to justice."
Authorities say they never gave up on the case. They followed up on almost 100 leads and consulted with FBI profilers trying to solve the murder.
"That's the highest priority we have in our office, solving a homicide. You have to stay motivated. Somebody out there's walking the streets thats a murderer.Thats motivation within itself," said Sgt. Langdon Sills from the prosecutor's office.
Officials would not discuss details of the case but confirm DNA on the victim's body matches Mertz.