Stanley Desmond James Stenton faced Darwin Local Court on Thursday on charges of sexual intercourse without consent and indecent dealing with a child under 16.
He failed to show up to court in 1998.
Stenton did not say anything during a brief appearance.
He also separately faced the Supreme Court on Thursday on three charges dating back earlier to 1995, including committing an indecent act on a child under 16, indecent dealings with a child under 16 and aggravated assault.
Northern Territory detectives travelled to Queensland this week to arrest Stenton.
The investigation was part of Operation Verto, in which NT Police is revisiting historical sexual assault court cases.
Stenton did not apply for bail and was remanded in custody by Judge Greg Cavanagh.
He is due back in court on March 11.