Prosecutors say DNA evidence tied Robert McCaffrey to the death of Lisa Marie McBride. She was 27 years old at the time of her death.
McCaffrey was arrested on April 10 in the Outer Banks of North Carolina.
During his court appearance Monday, he pleaded not guilty to murder, kidnapping and burglary charges.
He was led away back to a cell. He will remain in custody until his detention hearing to decide if he will stay in custody through his trial.
He has been the number one suspect in McBride's murder since she went missing from her Highland Lakes home in June 1990.
A hunter discovered her remains in the Delaware Water Gap in October of that same year.
Authorities say they were able to connect McCaffrey to the murder with the help of DNA evidence after his wife, Gail McCarthy, went missing in North Carolina in 2012.
He was and still is a suspect in her disappearance. He was arrested in 2014 and his DNA was collected for that case.
Back in New Jersey, McBride's remains were exhumed and DNA profiles that matched McCaffrey were discovered, police say.
The cold case had its first solid lead in decades thanks to the New Jersey State Police and its cold case unit.
McCaffrey spent 10 years in prison for obstruction in connection to his wife's case.
In the McBride case, McCaffrey's detention hearing is set for Monday.