A man who has previously been tried and acquitted of the murders of two Aboriginal children at Bowraville, on the NSW mid-north coast in the early 1990s, has once again been charged with their murder.

The man, who cannot be identified for legal reasons, appeared at Newcastle court on Thursday, over the deaths of four-year-old Evelyn Greenup and 16-year-old Clinton Speedy-Duroux.

Their bodies were found in bushland on the outskirts of the Bowraville Aboriginal Mission in northern NSW.

Map Bowraville, NSW

Whether the case proceeds any further will depend on an application to the NSW Court of Criminal Appeal by the Attorney-General, who is seeking to have the man re-tried.

Outside court, Clinton's father Thomas said the development was the best thing that had happened for a while.

"It's something we've wanted for a long time, it's really good to be here," he said.

"[We've] just got to keep fighting and keep going till we get there.

"I'm really glad it's come to this — [it's] been a long battle but hopefully we'll get there."

Their deaths have been among the state's most high-profile unsolved crimes, and the subject of significant media attention for the past quarter of a century.

The man who was charged on Thursday has already been acquitted of these murders at two separate trials in the past 20 years.

He stood trial for Clinton's murder in 1994 and Evelyn's murder in 2006 but was cleared both times.

NSW Police have alleged Evelyn and Clinton, along with 16-year-old Colleen Walker, were murdered by the same person within the space of a few months.

Police have alleged Colleen Walker was murdered by the same person who killed Evelyn and Clinton. ( AAP )

The three children disappeared within a five-month period from houses on the same street following parties at a section of Bowraville known as "the mission".

No-one has been charged over the suspected murder of Colleen, although a coroner has ruled she is dead.

The families of the three children have campaigned for 25 years to have all three cases heard together in a re-trial, but the state's double jeopardy laws have previously proved a stumbling block.

A major breakthrough came in May 2016, when NSW Attorney-General Gabrielle Upton made the decision to refer the application for a re-trial to the Court of Criminal Appeal, after NSW Police handed over a lengthy brief of evidence for the three cases to be heard together.